LMU BioDB 2017 - User contributions [en]

Lights, Camera, InterACTION! Deliverables

2017-12-15T06:22:22Z

Emmatyrnauer: /* GRNmap input and output workbooks */ organizing file deliverables

===Group Report and Presentation===
Presentation: [[Media:LCI Presentation.pdf]]

===Individual Statements===
[[Emma's Individual Statement]]

===Code and README===

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Final regulation matrix: [[Media:Final_regulationmatrix_trimmed.xlsx]]
# Input workbook: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]
# Output workbook after Matlab: [[Media:Matlab_output_17-genes_39-edges_teamINT_Sigmoid_estimation_output_copy.xlsx]]
# Weighted and unweighted GRNmap images: [[Media:GRNmap_images_emma_t.zip]]
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

File:GRNmap images emma t.zip

2017-12-15T06:21:46Z

Emmatyrnauer:

File:Matlab output 17-genes 39-edges teamINT Sigmoid estimation output copy.xlsx

2017-12-15T06:17:48Z

Emmatyrnauer: emma t deliverables

emma t deliverables

File:Final regulationmatrix trimmed.xlsx

2017-12-15T06:13:19Z

Emmatyrnauer: emma t deliverables

emma t deliverables

Emmatyrnauer Week 14

2017-12-15T02:03:25Z

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ clarification

==Electronic notebook for the continuation of Week 10 Data Analysis==
=== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ===

In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time. The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors. I explored this using the YEASTRACT database.

# I opened the gene list in Excel for the one of the significant profiles from my stem analysis (profile 45). I chose this cluster because it has a clear cold shock/recovery up/down pattern. It is also a large cluster.
#* I copied the list of gene IDs from my clipboard (C6:C585).
# I launched a web browser and went to the [http://www.yeastract.com/ YEASTRACT database].
#* On the left panel of the window, I clicked on the link to [http://www.yeastract.com/formrankbytf.php ''Rank by TF''].
#* I pasted the list of genes from the cluster (profile 45) into the box labeled ''ORFs/Genes''.
#* I checked the box for ''Check for all TFs''.
#* I accepted the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
#* I did '''''not''''' apply a filter for "Filter Documented Regulations by environmental condition".
#* I ranked genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
#* I clicked the ''Search'' button.
# I answered the following questions:
#* In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant". '''''How many transcription factors are green or "significant"?'''''
#**'''23 transcription factors are green/significant'''
#* '''''I copied the table of results from the web page and pasted it into a new Excel workbook to preserve the results.'''''
#** '''''I uploaded the Excel file to wiki linked to it here: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]].'''''
#** '''''Is your transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".''''' (Note: I didn't answer this because I was assigned the wt strain).
# For the mathematical model and GRNsight, I needed to define a ''gene regulatory network'' of transcription factors that regulatde other transcription factors. I used YEASTRACT to assist me with creating the network. I wanted to generate a network with approximately 15-30 transcription factors in it.
#* I selected from this list of "significant" transcription factors, which ones I was going to use to run the model. I used these transcription factors and added GLN3 because it was not already in my list. Justification: I chose all of the significant transcription factors from profile 45 because there were less than 30 and this would provide extra transcription factors for the network just in case some did not have connections to any of the others. List of transcription factors: ACE2, ARG80, GAT3, GCR2, GLN3, HAP4, INO4, MIG2, MSN2, NDT80, PDR3, SFP1, STB5, SUT1, UME6, YAP1, YHP1, YLR278C, and YOX1
#* I went back to the YEASTRACT database and followed the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''.
#* I copied and pasted the list of transcription factors I identified into both the "Transcription factors" field and the "Target ORF/Genes" field. I had to delete the spaces before each of the names for the regulatory network to generate properly.
#* I used the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"
#** I clicked the "Generate" button.
#** In the results window that appeared, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop. I renamed this file to "RegulationMatrix_yeastract_week10etf"


=== Visualizing My Gene Regulatory Network with GRNsight===

I analyzed the regulatory matrix file I generated above in Microsoft Excel and visualized it using GRNsight.
# First I needed to properly format the output file from YEASTRACT.
#* I opened the file in Excel. It did not open properly in Excel because a semicolon was used as the column delimiter instead of a comma. To fix this, I selected the entire Column A. I then went to the "Data" tab and selected "Text to columns". In the Wizard that appeared, I selected "Delimited" and clicked "Next". In the next window, I selected "Semicolon", and clicked "Next". In the next window, I left the data format at "General", and clicked "Finish". This now looked like a table with the names of the transcription factors across the top and down the first column and all of the zeros and ones distributed throughout the rows and columns. This is called an "adjacency matrix." If there is a "1" in the cell, that means there is a connection between the trancription factor in that row with that column.
#* I saved this file in Microsoft Excel workbook format (.xlsx).
#* I checked to see that all of the transcription factors in the matrix were connected to at least one of the other transcription factors by making sure that there was at least one "1" in a row or column for that transcription factor. If a factor was not connected to any other factor, I deleted its row and column from the matrix ( RIM101 and ASG1 were deleted). I made sure that I still had somewhere between 15 and 30 transcription factors in my network after this pruning (19).
#** I only deleted the transcription factor if there were all zeros in its column '''AND''' all zeros in its row.
#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), I needed to transpose the matrix. I inserted a new worksheet into my Excel file and named it "network". I went back to the previous sheet and selected the entire matrix and copied it. I went to my new worksheet and clickeded on the A1 cell in the upper left. I selected "Paste special" from the "Home" tab. In the window that appeared, I checked the box for "Transpose". This pasted my data with the columns transposed to rows and vice versa. This is necessary because I wanteded the transcription factors that were the "regulatORS" across the top and the "regulatEES" along the side.
#* The labels for the genes in the columns and rows needed to match. Thus, I deleted the "p" from each of the gene names in the columns. I also adjusted the case of the labels to make them all upper case.
#* In cell A1, I copied and pasted the text "rows genes affected/cols genes controlling".
#* Finally, for ease of working with the adjacency matrix in Excel, I wanted to alphabetize the gene labels both across the top and side.
#** I selected the area of the entire adjacency matrix.
#** I clicked the Data tab and clicked the custom sort button.
#** I sorted Column A alphabetically, being sure to exclude the header row.
#** I then sorted row 1 from left to right, excluding cell A1. In the Custom Sort window, I clicked on the options button and selected sort left to right, excluding column 1.
#* I named the worksheet containing my organized adjacency matrix "network" and Saved.
#**File: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
#**File after edits during class--trimming of regulatory network, explained on [[Emmatyrnauer Week 15]] (#5 is the final version): [[Media: REGULATIONMATRIXFINAL_ET.zip]]
# Now I visualized what these gene regulatory networks look like with the GRNsight software.
#* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network. I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results. I pasted it into my PowerPoint presentation from week 10 and uploaded a new version of the powerpoint including this screenshot to wiki: [[Media:Wt_profileimage_presentation_emmat.pptx]]

====Conclusion====
For the assignment this week, I used the YEASTRACT database to determine the connection between the regulation of different genes from the profile 45 genelist of the wild type microarray data. Yeastract allowed me to identify similarities in the expression pattern (through transcription factors) of the different genes. From profile 45, 23 transcription factors were identified as significant (these transcription factors regulated the most genes in the genelist of profile 45). I then used YEASTRACT to generate a regulation matrix of the 23 transcription factors--i also added GLN3 per the instructions. Finally, I made some adjustments to this regulation matrix (which was downloaded as a CSV file) to allow for it to be readable by GRNsight. I opened it in GRNsight which generated a graph of my network. This network graphically depicted the connections between the different genes.

==Acknowledgements==
#Dr. Dahlquist for teaching and assisting me with the data analysis
#The data analyst guild for assisting with the data analysis
# I copied and modified the instructions from the [[Week 10]] assignment page.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:38, 4 December 2017 (PST)

==References==
#LMU BioDB 2017. (2017). Week 10. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#YEASTRACT. Retrieved December 4, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
# GRNsight (2017) Retrieved December 4, 2017, from http://dondi.github.io/GRNsight/
{{Emmatyrnauer}}

Lights, Camera, InterACTION!

2017-12-15T02:01:14Z

Emmatyrnauer: /* Emma - Data Analysis */ signature

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]] '''-Coder'''
*[[user:emmatyrnauer|Emma Tyrnauer]] '''-Data Analyst'''
*[[user:kwrigh35|Katie Wright]] '''-Project Manager/Quality Assurance'''
*[[user:zvanysse|Zach Van Ysseldyke]] '''-Coder'''

==File Roundup==
*Final Presentation: [[media:LCI Presentation.pdf]]
*Week 11 presentation by Blair and Zach: [[media:The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf|The Secret Startup that Saved the Worst Website in America]]
*Week 12 presentation by Emma and Katie: [[media:Genome-wide expression analysis of yeast response during exposure to 4 degrees C.pdf|Genome-wide expression analysis of yeast response during exposure to 4 degrees C]]
*Microarray data excel spreadsheet (corrected) : [[Media:Wt_Microarraydata_ET.zip]]
[[Lights, Camera, InterACTION! Deliverables]]

==Team Schedule== 
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' <s> C: PPT Presentation PM/DA: Journal Articles</s>
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' <s>C: Complete setup steps (Milestones 0-4) PM/DA: Journal Club Presentations DA: Week 8 and Week 10 edits</s>
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' <s>C: First Integration projected completion</s> <s>PM: Check in with team DA: </s>
|'''29'''
|'''30''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA:</s>
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' <s>C: Check in with groups, and further integrate as needed.</s> PM: Check in with team <s>DA: complete week 10 data analysis</s>
|'''6'''
|'''7''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA: </s>
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' <s>Final group Presentation ''2:00-4:00PM''</s>
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==
===Week 11===
====Katie - PM/QA====
For this week, I worked with [[user:emmatyrnauer|Emma]] to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my [[kwrigh35 Week 11|Week 11]] journal page.
#'''What worked?''' Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
#'''What didn't work?''' I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
#'''What will I do next to fix what didn't work?''' I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

====Emma - Data Analysis====
This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: [[Emmatyrnauer Week 11]]. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.
# Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
# There wasn't really anything that didn't work.
# Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:26, 13 November 2017 (PST)

====Blair - Coder====
This week Zach and I created the Powerpoint presentation about ''The secret startup that saved the worst website in America'' article. We created individual outlines of the article on our respective pages, mine is as follows: [[Bhamilton18 Week 11]]. Our presentation is linked here: [[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
#Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
#Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
#For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 23:35, 13 November 2017 (PST)

====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]] 
[[Zvanysse Week 11]] 
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.
#'''Things that went well:''' Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
#'''Things that didn't go well:''' Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
#Like I said above, we will plan out exact times earlier on in the week that we can meet up
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 23:44, 13 November 2017 (PST) 

===Week 12===
====Katie - PM/QA====
Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my [[kwrigh35 Week 12|Week 12]] page. The presentation can be found in the "file roundup" section of this page.
#'''What worked?'''Emma and I met up outside of class to work on the assignment, which was really helpful.
#'''What didn't work?'''I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
#'''What will I do next to fix what didn't work?'''I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

====Emma - Data Analysis====
This week I made all the corrections listed on the talk page of my user page for both [[Emmatyrnauer Week 8]] and [[Emmatyrnauer Week 10]]. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, [[Emmatyrnauer Week 12]]. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."
#'''What worked well:''' It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
#'''What didn't worked well:''' This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
#'''What will we do to fix what didn't work?''' I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:03, 20 November 2017 (PST)

====Blair - Coder====
As mentioned on my electronic notebook, [[Bhamilton18 Week 12]], this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.
#'''What worked well:''' Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
#'''What didn't worked well:''' We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
#'''What will we do to fix what didn't work?''' Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 19:15, 20 November 2017 (PST)
====Zach - Coder====
This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page. 
[[Zvanysse Week 12]] 
#'''Things that went well:''' we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
#'''Things that didn't go well:''' We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
#'''What we will do to fix it:''' We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

===Week 14===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: [[Emmatyrnauer Week 14]].
#'''Things that went well:''' It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
#'''Things that didn't go well:''' Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
#'''What we will do to fix it:''' For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:31, 4 December 2017 (PST)

====Blair - Coder====
This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, [[Bhamilton18 Week 14]], we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.
#'''Things that went well:''' Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
#'''Things that didn't go well:''' Working in D3 syntax has been difficult to progress in certain deliverables.
#'''What we will do to fix it:''' In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 21:25, 4 December 2017 (PST)
====Zach - Coder====
This week Blair and I worked on the first integration by merging through github as well as working on the right click function. This function enabled us to right click and automatically link the gene that was clicked on to that particular gene page. We connected by texting as well as meeting up in person before committing our week's work to make sure that we were on the same page. We mentioned this on my electronic notebook, [[Zvanysse Week 14]]. We collaborated with Dr. Dionisio to work out some of the D3 technical syntax problems that came about. Emma worked on progressing on the data analysis for the gene wild type and Katie make sure that everyone was on task.
#'''What went well:''' Our communication and procrastination was overall much better. Collaborating with other teams went smoothly and connecting with Dr. Dionisio for syntax went well as the problem was diagnosed soon after it became about.
#'''What Didn't go well:''' Working with D3 was a little difficult because the syntax ultimately changed for the API. This was unforeseen so it was a little frustrating.
#'''How will we fix this:''' When it comes to syntax problems, we will be more in communication with Dr. Dionisio 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 21:36, 4 December 2017 (PST)

===Week 15===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I completed last steps for data analysis including the visualization of my gene network in GRNsight. Specifics of steps performed and associated files can be accessed on [[Emmatyrnauer Week 15]]. I also met up with my teammates prior to the presentation to complete the powerpoint as well as practice a few times. Once the presentation was complete, our entire group communicated over text to finish the final deliverables for this project (i.e. the group report, individual statements, etc.) I was really happy with how things turned out!

[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 18:01, 14 December 2017 (PST)

====Blair - Coder====
For the final week of the project [[User:Zvanysse|Zach]] and I worked heavy on the integration portion of the coding. We inputed the data into the overall info.html page, referenced the gene ids of the following databases: NCBI, SGD, UniProt, JASPAR and Ensembl, and finally met with each coding groups to finalize the final pull of code from everyone. More details on the code and final project can be read on my electronic lab notebook: [[Bhamilton18 Week 15]]. For the final project deliverables, Katie, Emma, Zach and I met twice to collaborate on the presentation, read over our slides and add in details/pictures. Lastly, we communicated through text message and google slides/docs to complete the powerpoint and final paper.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 22:04, 13 December 2017 (PST)
====Zach - Coder====

==Bibliography==
===Paper 1===
Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. ''Cryobiology'', 46(3), 230-237.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
* PubMed Central: not available
* Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
* Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
* Copyright: 2003 by Science Direct; article is not Open Access
* Publisher: Elsevier Science
* Availability: online at www.sciencedirect.com
* Did LMU pay a fee for this article: yes

===Paper 2===
Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
* PubMed Central: not available
* Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
* Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
* Copyright: 2005 by Springer-Verlag; article is not Open Access
* Publisher: Springer-Verlag
* Availability: online
* Did LMU pay a fee for this article: yes

===Paper 3===
Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

'''PubMed Abstract:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

'''PubMed Central:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

'''Publisher Full Text (HTML):''' unavailable

'''Publisher Full Text (PDF):''' http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

'''Copyright:''' Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

'''Publisher:''' Hindawi Publishing Corporation

'''Availability:''' Open access

'''Did LMU pay a fee for this article:''' no

===Paper 4===
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

'''PubMed Abstract: ''' https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

'''PubMed Central: ''' not available

'''Publisher Full Text (HTML): ''' http://www.jbc.org/content/277/51/50015.long

'''Publisher Full Text (PDF): ''' http://www.jbc.org/content/277/51/50015.full.pdf

'''Copyright: ''' "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

'''Publisher: ''' American Society for Biochemistry and Molecular Biology

'''Availability: '''All articles from this journal are free 1 year after publishing.

'''Did LMU pay a fee for this article:''' No.

==Acknowledgments==
#Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
#*WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
#We utilized the Calendar outline from the [[JASPAR the Friendly Ghost]] page, but changed the milestone/tasks due.

==References==
*Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/
*Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

{{template:Pugs Not Drugs}}

{{GRNsight Gene Page Project Links}}

Lights, Camera, InterACTION!

2017-12-15T01:59:58Z

Emmatyrnauer: /* Emma - Data Analysis */ adding executive summary

[[File:PugNotDrugsLogo.png|400px|thumb|right|Pugs Not Drugs Logo]]

==Team Members==
*[[user:bhamilton18|Blair Hamilton]] '''-Coder'''
*[[user:emmatyrnauer|Emma Tyrnauer]] '''-Data Analyst'''
*[[user:kwrigh35|Katie Wright]] '''-Project Manager/Quality Assurance'''
*[[user:zvanysse|Zach Van Ysseldyke]] '''-Coder'''

==File Roundup==
*Final Presentation: [[media:LCI Presentation.pdf]]
*Week 11 presentation by Blair and Zach: [[media:The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf|The Secret Startup that Saved the Worst Website in America]]
*Week 12 presentation by Emma and Katie: [[media:Genome-wide expression analysis of yeast response during exposure to 4 degrees C.pdf|Genome-wide expression analysis of yeast response during exposure to 4 degrees C]]
*Microarray data excel spreadsheet (corrected) : [[Media:Wt_Microarraydata_ET.zip]]
[[Lights, Camera, InterACTION! Deliverables]]

==Team Schedule== 
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' <s> C: PPT Presentation PM/DA: Journal Articles</s>
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' <s>C: Complete setup steps (Milestones 0-4) PM/DA: Journal Club Presentations DA: Week 8 and Week 10 edits</s>
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' <s>C: First Integration projected completion</s> <s>PM: Check in with team DA: </s>
|'''29'''
|'''30''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA:</s>
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' <s>C: Check in with groups, and further integrate as needed.</s> PM: Check in with team <s>DA: complete week 10 data analysis</s>
|'''6'''
|'''7''' <s>C: Check in with other groups about progress</s> <s>PM: Check in with team DA: </s>
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' <s>Final group Presentation ''2:00-4:00PM''</s>
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==
===Week 11===
====Katie - PM/QA====
For this week, I worked with [[user:emmatyrnauer|Emma]] to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my [[kwrigh35 Week 11|Week 11]] journal page.
#'''What worked?''' Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
#'''What didn't work?''' I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
#'''What will I do next to fix what didn't work?''' I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

====Emma - Data Analysis====
This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: [[Emmatyrnauer Week 11]]. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.
# Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
# There wasn't really anything that didn't work.
# Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:26, 13 November 2017 (PST)

====Blair - Coder====
This week Zach and I created the Powerpoint presentation about ''The secret startup that saved the worst website in America'' article. We created individual outlines of the article on our respective pages, mine is as follows: [[Bhamilton18 Week 11]]. Our presentation is linked here: [[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]]
#Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
#Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
#For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 23:35, 13 November 2017 (PST)

====Zach - Coder====
[[Media: The_Secret_Startup_that_Saved_the_Worst_Website_in_America.pdf | Zach and Blair's Powerpoint]] 
[[Zvanysse Week 11]] 
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.
#'''Things that went well:''' Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
#'''Things that didn't go well:''' Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
#Like I said above, we will plan out exact times earlier on in the week that we can meet up
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 23:44, 13 November 2017 (PST) 

===Week 12===
====Katie - PM/QA====
Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my [[kwrigh35 Week 12|Week 12]] page. The presentation can be found in the "file roundup" section of this page.
#'''What worked?'''Emma and I met up outside of class to work on the assignment, which was really helpful.
#'''What didn't work?'''I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
#'''What will I do next to fix what didn't work?'''I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

====Emma - Data Analysis====
This week I made all the corrections listed on the talk page of my user page for both [[Emmatyrnauer Week 8]] and [[Emmatyrnauer Week 10]]. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, [[Emmatyrnauer Week 12]]. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."
#'''What worked well:''' It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
#'''What didn't worked well:''' This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
#'''What will we do to fix what didn't work?''' I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 20:03, 20 November 2017 (PST)

====Blair - Coder====
As mentioned on my electronic notebook, [[Bhamilton18 Week 12]], this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.
#'''What worked well:''' Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
#'''What didn't worked well:''' We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
#'''What will we do to fix what didn't work?''' Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.
[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 19:15, 20 November 2017 (PST)
====Zach - Coder====
This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page. 
[[Zvanysse Week 12]] 
#'''Things that went well:''' we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
#'''Things that didn't go well:''' We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
#'''What we will do to fix it:''' We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

===Week 14===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: [[Emmatyrnauer Week 14]].
#'''Things that went well:''' It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
#'''Things that didn't go well:''' Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
#'''What we will do to fix it:''' For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:31, 4 December 2017 (PST)

====Blair - Coder====
This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, [[Bhamilton18 Week 14]], we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.
#'''Things that went well:''' Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
#'''Things that didn't go well:''' Working in D3 syntax has been difficult to progress in certain deliverables.
#'''What we will do to fix it:''' In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 21:25, 4 December 2017 (PST)
====Zach - Coder====
This week Blair and I worked on the first integration by merging through github as well as working on the right click function. This function enabled us to right click and automatically link the gene that was clicked on to that particular gene page. We connected by texting as well as meeting up in person before committing our week's work to make sure that we were on the same page. We mentioned this on my electronic notebook, [[Zvanysse Week 14]]. We collaborated with Dr. Dionisio to work out some of the D3 technical syntax problems that came about. Emma worked on progressing on the data analysis for the gene wild type and Katie make sure that everyone was on task.
#'''What went well:''' Our communication and procrastination was overall much better. Collaborating with other teams went smoothly and connecting with Dr. Dionisio for syntax went well as the problem was diagnosed soon after it became about.
#'''What Didn't go well:''' Working with D3 was a little difficult because the syntax ultimately changed for the API. This was unforeseen so it was a little frustrating.
#'''How will we fix this:''' When it comes to syntax problems, we will be more in communication with Dr. Dionisio 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 21:36, 4 December 2017 (PST)

===Week 15===
====Katie - PM/QA====
====Emma - Data Analysis====
This week I completed last steps for data analysis including the visualization of my gene network in GRNsight. Specifics of steps performed and associated files can be accessed on [[Emmatyrnauer Week 15]]. I also met up with my teammates prior to the presentation to complete the powerpoint as well as practice a few times. Once the presentation was complete, our entire group communicated over text to finish the final deliverables for this project (i.e. the group report, individual statements, etc.) I was really happy with how things turned out!
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 17:59, 14 December 2017 (PST)

====Blair - Coder====
For the final week of the project [[User:Zvanysse|Zach]] and I worked heavy on the integration portion of the coding. We inputed the data into the overall info.html page, referenced the gene ids of the following databases: NCBI, SGD, UniProt, JASPAR and Ensembl, and finally met with each coding groups to finalize the final pull of code from everyone. More details on the code and final project can be read on my electronic lab notebook: [[Bhamilton18 Week 15]]. For the final project deliverables, Katie, Emma, Zach and I met twice to collaborate on the presentation, read over our slides and add in details/pictures. Lastly, we communicated through text message and google slides/docs to complete the powerpoint and final paper.

[[User:Bhamilton18|Bhamilton18]] ([[User talk:Bhamilton18|talk]]) 22:04, 13 December 2017 (PST)
====Zach - Coder====

==Bibliography==
===Paper 1===
Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. ''Cryobiology'', 46(3), 230-237.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
* PubMed Central: not available
* Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
* Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
* Copyright: 2003 by Science Direct; article is not Open Access
* Publisher: Elsevier Science
* Availability: online at www.sciencedirect.com
* Did LMU pay a fee for this article: yes

===Paper 2===
Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. ''Extremophiles'', 10(2), 117-128.
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
* PubMed Central: not available
* Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
* Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
* Copyright: 2005 by Springer-Verlag; article is not Open Access
* Publisher: Springer-Verlag
* Availability: online
* Did LMU pay a fee for this article: yes

===Paper 3===
Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

'''PubMed Abstract:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

'''PubMed Central:''' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

'''Publisher Full Text (HTML):''' unavailable

'''Publisher Full Text (PDF):''' http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

'''Copyright:''' Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

'''Publisher:''' Hindawi Publishing Corporation

'''Availability:''' Open access

'''Did LMU pay a fee for this article:''' no

===Paper 4===
Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

'''PubMed Abstract: ''' https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

'''PubMed Central: ''' not available

'''Publisher Full Text (HTML): ''' http://www.jbc.org/content/277/51/50015.long

'''Publisher Full Text (PDF): ''' http://www.jbc.org/content/277/51/50015.full.pdf

'''Copyright: ''' "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

'''Publisher: ''' American Society for Biochemistry and Molecular Biology

'''Availability: '''All articles from this journal are free 1 year after publishing.

'''Did LMU pay a fee for this article:''' No.

==Acknowledgments==
#Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
#*WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
#We utilized the Calendar outline from the [[JASPAR the Friendly Ghost]] page, but changed the milestone/tasks due.

==References==
*Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/
*Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

{{template:Pugs Not Drugs}}

{{GRNsight Gene Page Project Links}}

Emmatyrnauer Week 15

2017-12-15T01:54:52Z

Emmatyrnauer: /* Electronic Notebook */ typo

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose ends/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ([[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file (within [[Media:GRNsight_inputoutput_excelandimages.zip‎]]) as well as individual .jpg images for each gene ([[Media:Emmat_gene_jpg_matlab.zip]]). The output matrix file was opened in GRNsight and produced Figure 2. Pink arrows indicate induction/upregulation while blue lines with bars indicate repression/downregulation. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many of the genes belonging to this network. Furthermore, some genes are regulated by one gene while others are regulated by multiple (Fig. 2). It is also notable that some of the genes that are repressed, are also induced (Fig. 2). This suggests a form of very specific regulation where the cell may be sensitive to subtle changes in expression of these genes. As a result, the cell utilizes differing pathways for their regulation.
[[File:Emmat_unweighted_gene_network.png|500px|thumb|right|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|500px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#YEASTRACT. Retrieved December 7, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
#GRNsight (2017) Retrieved December 7, 2017, from http://dondi.github.io/GRNsight/
#Matlab. Retrieved December 7, 2017, from LMU's computer lab (https://www.mathworks.com/products/matlab.html)

{{Emmatyrnauer}}

Emmatyrnauer Week 15

2017-12-15T01:53:32Z

Emmatyrnauer: /* Electronic Notebook */ adding additional file links

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose ends/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ([[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file (within [[Media:GRNsight_inputoutput_excelandimages.zip‎]]) as well as individual .jpg images for each gene ([[Media:Emmat_gene_jpg_matlab.zip]]). The output matrix file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many of the genes belonging to this network. Furthermore, some genes are regulated by one gene while others are regulated by multiple (Fig. 2). It is also notable that some of the genes that are repressed, are also induced (Fig. 2). This suggests a form of very specific regulation where the cell may be sensitive to subtle changes in expression of these genes. As a result, the cell utilizes differing pathways for their regulation.
[[File:Emmat_unweighted_gene_network.png|500px|thumb|right|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|500px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#YEASTRACT. Retrieved December 7, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
#GRNsight (2017) Retrieved December 7, 2017, from http://dondi.github.io/GRNsight/
#Matlab. Retrieved December 7, 2017, from LMU's computer lab (https://www.mathworks.com/products/matlab.html)

{{Emmatyrnauer}}

Emma's Individual Statement

2017-12-15T01:46:53Z

Emmatyrnauer: /* Assessment of Project */ final touches

==Individual Assessment and Reflection==
===Statement of Work===
'''Describe exactly what you did on the project (provide links to work).'''
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly! We all contributed our specific parts to the final group report and Katie, our project manager/quality assurance made sure that everything required was there.
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization of the project was good. Each week I made sure to document everything that I did on my wiki pages (and so did my group members). I added deliverables to the deliverables page as I completed them and did not wait until the last minute to complete anything.
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
'''What did you learn?'''
* '''With your head:''' Completing this project, I learned a lot about interpreting microarray data with the ANOVA test and utilizing excel for data analysis (I have used it for classes here and there but none at the same extent). I also learned about how cold shock has an effect on gene expression and the effect is represented thorough plots of expression change over time. Different clusters are regulated by different transcription factors, which is why these clusters have differently shaped graphs.
*'''With your heart:''' This project really gave me an appreciation for coding and computer science. Zach and Blair worked extremely hard trying to integrate all of the information from the other teams, which was a lot of hard work. Yet, they were still able to get all the assignments in on time and were very good at communicating with the rest of the group. This project also gave me an appreciation for teamwork as it was a lot of work! However, we all did our parts to contribute to the final product.
*'''With your hands:''' Technically, I learned how to perform the ANOVA in excel and correct the associated p-values--the Benjamini and Hochberg-corrected p<0.05, and the Bonferroni-corrected p<0.05. I also learned how to utilize STEM for clustering, and Yeastract and GRNsight for network visualization.
*'''What lesson will you take away from this project that you will still use a year from now?''' This project felt very much like a job--having different types of team members and a project manager. I will most likely take away being able to work in a group setting with members that have different skill sets and working together to complete project deliverables.

{{Emmatyrnauer}}

Emma's Individual Statement

2017-12-15T01:40:21Z

Emmatyrnauer: /* Reflection on the Process */ edition

==Individual Assessment and Reflection==
===Statement of Work===
'''Describe exactly what you did on the project (provide links to work).'''
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
'''What did you learn?'''
* '''With your head:''' Completing this project, I learned a lot about interpreting microarray data with the ANOVA test and utilizing excel for data analysis (I have used it for classes here and there but none at the same extent). I also learned about how cold shock has an effect on gene expression and the effect is represented thorough plots of expression change over time. Different clusters are regulated by different transcription factors, which is why these clusters have differently shaped graphs.
*'''With your heart:''' This project really gave me an appreciation for coding and computer science. Zach and Blair worked extremely hard trying to integrate all of the information from the other teams, which was a lot of hard work. Yet, they were still able to get all the assignments in on time and were very good at communicating with the rest of the group. This project also gave me an appreciation for teamwork as it was a lot of work! However, we all did our parts to contribute to the final product.
*'''With your hands:''' Technically, I learned how to perform the ANOVA in excel and correct the associated p-values--the Benjamini and Hochberg-corrected p<0.05, and the Bonferroni-corrected p<0.05. I also learned how to utilize STEM for clustering, and Yeastract and GRNsight for network visualization.
*'''What lesson will you take away from this project that you will still use a year from now?''' This project felt very much like a job--having different types of team members and a project manager. I will most likely take away being able to work in a group setting with members that have different skill sets and working together to complete project deliverables.

{{Emmatyrnauer}}

Emmatyrnauer Week 15

2017-12-15T01:34:55Z

Emmatyrnauer: /* Electronic Notebook */ editing

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose ends/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ([[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file. This file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many of the genes belonging to this network. Furthermore, some genes are regulated by one gene while others are regulated by multiple (Fig. 2). It is also notable that some of the genes that are repressed, are also induced (Fig. 2). This suggests a form of very specific regulation where the cell may be sensitive to subtle changes in expression of these genes. As a result, the cell utilizes differing pathways for their regulation.
[[File:Emmat_unweighted_gene_network.png|500px|thumb|right|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|500px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#YEASTRACT. Retrieved December 7, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
#GRNsight (2017) Retrieved December 7, 2017, from http://dondi.github.io/GRNsight/
#Matlab. Retrieved December 7, 2017, from LMU's computer lab (https://www.mathworks.com/products/matlab.html)

{{Emmatyrnauer}}

Emmatyrnauer Week 15

2017-12-15T00:06:08Z

Emmatyrnauer: /* References */ adding references

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose end/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ( [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file. This file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many other genes.

[[File:Emmat_unweighted_gene_network.png|500px|thumb|right|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|500px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#YEASTRACT. Retrieved December 7, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
#GRNsight (2017) Retrieved December 7, 2017, from http://dondi.github.io/GRNsight/
#Matlab. Retrieved December 7, 2017, from LMU's computer lab (https://www.mathworks.com/products/matlab.html)

{{Emmatyrnauer}}

Emmatyrnauer Week 15

2017-12-15T00:02:45Z

Emmatyrnauer: /* Electronic Notebook */ making images larger

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose end/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ( [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file. This file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many other genes.

[[File:Emmat_unweighted_gene_network.png|500px|thumb|right|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|500px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#Yeastract
#Matlab
GRNsight

{{Emmatyrnauer}}

Emmatyrnauer Week 15

2017-12-15T00:02:05Z

Emmatyrnauer: moving images

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose end/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ( [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file. This file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many other genes.

[[File:Emmat_unweighted_gene_network.png|400px|thumb|right|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|400px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#Yeastract
#Matlab
GRNsight

{{Emmatyrnauer}}

Emmatyrnauer Week 15

2017-12-15T00:01:01Z

Emmatyrnauer: /* Electronic Notebook */ linking to images

==Electronic Notebook==
In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose end/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in [[Media: REGULATIONMATRIXFINAL_ET.zip]], with the final version being #5 (this media file has also been linked to on [[Emmatyrnauer Week 14]] as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ( [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx | 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file. This file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many other genes.
[[File:Emmat_unweighted_gene_network.png|400px|thumb|left|Figure 1. Unweighted network]]
[[File:Emmat_weighted_gene_network.png|400px|thumb|right|Figure 2. Weighted network]]

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#Yeastract
#Matlab
GRNsight

{{Emmatyrnauer}}

File:Emmat weighted gene network.png

2017-12-14T23:59:18Z

Emmatyrnauer: week 15

week 15

File:Emmat unweighted gene network.png

2017-12-14T23:58:30Z

Emmatyrnauer: week 15

week 15

Emmatyrnauer Week 15

2017-12-14T23:54:50Z

Emmatyrnauer: /* Electronic Notebook */ progress with electronic notebook

Emmatyrnauer Week 15

2017-12-14T18:49:32Z

Emmatyrnauer: /* Electronic Notebook */ progress with electronic notebook

Template:Emmatyrnauer

2017-12-14T16:47:15Z

Emmatyrnauer: /* Links */ adding week 15 links

===Links===
#[[User:Emmatyrnauer|My User Page]]
#List of Assignments
#*[[Week 1]]
#*[[Week 2]]
#*[[Week 3]]
#*[[Week 4]]
#*[[Week 5]]
#*[[Week 6]]
#*[[Week 7]]
#*[[Week 8]]
#*[[Week 9]]
#*[[Week 10]]
#*[[Week 11]]
#*[[Week 12]]
#* no Week 13
#*[[Week 14]]
#*[[Week 15]]
#List of Journal Entries
#*[[User:Emmatyrnauer|Emmatyrnauer Week 1]]
#*[[Emmatyrnauer Week 2]]
#*[[Emmatyrnauer Week 3]]
#*[[Emmatyrnauer Week 4]]
#*[[Influenza Research Database | Emmatyrnauer Week 5]]
#*[[Emmatyrnauer Week 6]]
#*[[Emmatyrnauer Week 7]]
#*[[Emmatyrnauer Week 8]]
#*[[Emmatyrnauer Week 9]]
#*[[Emmatyrnauer Week 10]]
#*[[Emmatyrnauer Week 11]]
#*[[Emmatyrnauer Week 12]]
#* no Week 13
#*[[Emmatyrnauer Week 14]]
#*[[Emmatyrnauer Week 15]]
#List of Shared Journal Entries
#*[[Class Journal Week 1]]
#*[[Class Journal Week 2]]
#*[[Class Journal Week 3]]
#*[[Class Journal Week 4]]
#*[[Class Journal Week 5]]
#*[[Class Journal Week 6]]
#*[[Class Journal Week 7]]
#*[[Class Journal Week 8]]
#*[[Class Journal Week 9]]
#*[[Class Journal Week 10]]
#*[[Lights, Camera, InterACTION! | Group Journal Week 11]]
#*[[Lights, Camera, InterACTION! | Group Journal Week 12]]
#* no week 13
#*[[Lights, Camera, InterACTION! | Group Journal Week 14]] (executive summary)
#*[[Lights, Camera, InterACTION! | Group Journal Week 14]] (executive summary)
#*[[Lights, Camera, InterACTION! | Group Journal Week 15]] (executive summary)
[[Category: Journal Entry]]

Emma's Individual Statement

2017-12-14T16:39:40Z

Emmatyrnauer: /* Individual Assessment and Reflection */ adding template

==Individual Assessment and Reflection==
===Statement of Work===
'''Describe exactly what you did on the project (provide links to work).'''
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
'''What did you learn?'''
* '''With your head:''' Completing this project, I learned a lot about interpreting microarray data with the ANOVA and utilizing excel for data analysis (I have used it for classes here and there but none at the same extent). I also learned about how cold shock has an effect on gene expression and the effect is represented thorough plots of expression change over time. Different clusters are regulated by different transcription factors which is why these clusters have differently shaped graphs.
*'''With your heart:''' This project really gave me an appreciation for coding and computer science. Zach and Blair worked extremely hard trying to integrate all of the information from the other teams, which was a lot of hard work. Yet, they were still able to get all the assignments in on time and were very good at communicating with the rest of the group
*'''With your hands:''' Technically, I learned how to perform the ANOVA in excel and correct the associated p-values--the Benjamini and Hochberg-corrected p<0.05, and the Bonferroni-corrected p<0.05. I also learned how to utilize STEM for clustering, and Yeastract and GRNsight for network visualization.
*'''What lesson will you take away from this project that you will still use a year from now?''' This project felt very much like a job having different types of team members and a project manager. I will most likely take away being able to work in a group setting with members that have different skill sets and working together to complete project deliverables.

{{Emmatyrnauer}}

Emma's Individual Statement

2017-12-14T16:38:41Z

Emmatyrnauer: /* Reflection on the Process */ progress

==Individual Assessment and Reflection==
===Statement of Work===
'''Describe exactly what you did on the project (provide links to work).'''
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
'''What did you learn?'''
* '''With your head:''' Completing this project, I learned a lot about interpreting microarray data with the ANOVA and utilizing excel for data analysis (I have used it for classes here and there but none at the same extent). I also learned about how cold shock has an effect on gene expression and the effect is represented thorough plots of expression change over time. Different clusters are regulated by different transcription factors which is why these clusters have differently shaped graphs.
*'''With your heart:''' This project really gave me an appreciation for coding and computer science. Zach and Blair worked extremely hard trying to integrate all of the information from the other teams, which was a lot of hard work. Yet, they were still able to get all the assignments in on time and were very good at communicating with the rest of the group
*'''With your hands:''' Technically, I learned how to perform the ANOVA in excel and correct the associated p-values--the Benjamini and Hochberg-corrected p<0.05, and the Bonferroni-corrected p<0.05. I also learned how to utilize STEM for clustering, and Yeastract and GRNsight for network visualization.
*'''What lesson will you take away from this project that you will still use a year from now?''' This project felt very much like a job having different types of team members and a project manager. I will most likely take away being able to work in a group setting with members that have different skill sets and working together to complete project deliverables.

Emma's Individual Statement

2017-12-14T07:08:34Z

Emmatyrnauer: /* Reflection on the Process */ bolding

==Individual Assessment and Reflection==
===Statement of Work===
'''Describe exactly what you did on the project (provide links to work).'''
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
'''What did you learn?'''
* '''With your head'''
*'''With your heart''' (personal qualities and teamwork qualities that make things work or not work)?
*'''With your hands''' (technical skills)?
*'''What lesson will you take away from this project that you will still use a year from now?'''

Emma's Individual Statement

2017-12-14T07:06:14Z

Emmatyrnauer: /* Statement of Work */ bolding

==Individual Assessment and Reflection==
===Statement of Work===
'''Describe exactly what you did on the project (provide links to work).'''
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Emma's Individual Statement

2017-12-14T07:05:51Z

Emmatyrnauer: /* Assessment of Project */ bolding

==Individual Assessment and Reflection==
===Statement of Work===
Describe exactly what you did on the project (provide links to work).
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#'''Give an objective assessment of the success of your project workflow and teamwork.'''
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* '''What worked and what didn't work?'''
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* '''What would you do differently if you could do it all over again?'''
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# '''Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''
#* '''Content: What is the quality of the work?'''
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!
#* '''Organization: Comment on the organization of the project and of your group's wiki pages.'''
#** Our work and organization
#* '''Completeness: Did your team achieve all of the project objectives? Why or why not?'''
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Emma's Individual Statement

2017-12-14T07:03:57Z

Emmatyrnauer: /* Assessment of Project */ bolding

==Individual Assessment and Reflection==
===Statement of Work===
Describe exactly what you did on the project (provide links to work).
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#Give an objective assessment of the success of your project workflow and teamwork.
'''#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.'''
#* What worked and what didn't work?
'''#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).'''
#* What would you do differently if you could do it all over again?
'''#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.'''
# Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
#* Content: What is the quality of the work?
'''#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Blair and Zach seemed to work perfectly!'''
#* Organization: Comment on the organization of the project and of your group's wiki pages.
'''#** Our work and organization'''
#* Completeness: Did your team achieve all of the project objectives? Why or why not?
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Emma's Individual Statement

2017-12-14T06:39:46Z

Emmatyrnauer: /* Assessment of Project */ progress

==Individual Assessment and Reflection==
===Statement of Work===
Describe exactly what you did on the project (provide links to work).
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#Give an objective assessment of the success of your project workflow and teamwork.
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* What worked and what didn't work?
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* What would you do differently if you could do it all over again?
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break). I would also try to be a little more organized with all of the data because I initially found myself confused about which files were supposed to linked on the deliverables page.
# Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
#* Content: What is the quality of the work?
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality. The right click function demonstrated by Katie and Zach seemed to work perfectly!
#* Organization: Comment on the organization of the project and of your group's wiki pages.
#** Our work and organization
#* Completeness: Did your team achieve all of the project objectives? Why or why not?
#** My team did achieve all of the project objectives! We were all very responsible for each of our contributions and double checked to ensure that all the deliverables were completed.

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Emma's Individual Statement

2017-12-14T06:09:36Z

Emmatyrnauer: /* Assessment of Project */ progress answering questions

==Individual Assessment and Reflection==
===Statement of Work===
Describe exactly what you did on the project (provide links to work).
* For this project I served as the data analyst. During the first week (week 11) I started off by creating an annotated bibliography of scientific journal articles dealing with yeast, cold shock, and microarray data. This bibliography was created with my group's project manager, [[User:Kwrigh35|Katie]], and can be accessed on [[Emmatyrnauer Week 11]]. This week also consisted of constructing our group's individual page, [[Lights, Camera, InterACTION!]].
* During week 12, Katie and I worked on our journal club presentation. Each of us constructed individual outlines of the paper we had been assigned and then met up to write and divide up our journal club presentation. Prior to the class during which we were supposed to present, we met up to practice a few times. The outline that I wrote and the presentation that we made can be accessed on [[Emmatyrnauer Week 12]]. This was also the week that I completed all of the corrections that I needed to make on my week 8 individual page ([[Emmatyrnauer Week 8]]) and my week 10 individual page ([[Emmatyrnauer Week 10]]). Dr. Dahlquist had listed out all of the necessary corrections on the talk page of my user page ([[User:Emmatyrnauer]]), so I went through this list and checked off corrections as they were made.
* We had week 13 off due to Thanksgiving, yay! :)
* During week 14, I completed the week 10 data analysis including using Yeastract to infer transcription factors and visualizing my gene regulatory network with GRNsight. Documentation of procedure, resulting files, and conclusion can be accessed on [[Emmatyrnauer Week 14]].
* Week 15 was the last week to work on the group project. Final steps of data analysis were completed with a great deal of help from Dr. Dahlquist. Adjustments were made to the list of transcription factors that were returned from Yeastract. This included trimming of the network because it was too large, as well as ensuring that specific genes requested by Dr. Dahlquist were included in the network. Dr. Dahlquist ran Matlab with the data that I provided her and I retrieved that output file containing the weighted gene network the following day. Overview of this process with corresponding files can be accessed on [[Emmatyrnauer Week 15]].
* During finals week, my group met to work on our group presentation (which I thought went really well). Each of us focused on presenting the work we had individually accomplished for the project and collaborated on future directions for research and conclusions. Following the completion of the presentation, we completed the paper and the rest of the deliverables (which all can be accessed on [[Lights, Camera, InterACTION! Deliverables]] page.

===Assessment of Project===
#Give an objective assessment of the success of your project workflow and teamwork.
#* Overall, I think that my group worked extremely well together at completing the necessary tasks and deliverables for this project. While there were some miscommunications here and there, everything was sorted out efficiently and all group members were responsible and available to help each other.
#* What worked and what didn't work?
#**Being able to have everyone's strengths utilized was very beneficial in the completion of this project. I liked how guilds for each of the different job titles were formed as this allowed for any questions we had to be quickly answered. Furthermore, I thought that Katie did a really good job of staying on top of the material and deliverables that were required and organizing the tasks that needed to be complete. I didn't really notice any struggles within our team (other than a minor miscommunication between the coders and project manager which got sorted out really well). However, I do remember feeling extremely overwhelmed in week 12 when I thought that all the corrections to my week 8 and week 10 individual pages had to be done on the same day that I had to present my journal club paper. However, when I got to class, I realized that I was the only data analyst that had made these corrections and could have spread out the work a little better (I was being a little too ambitious).
#* What would you do differently if you could do it all over again?
#**If I could do this project all over again, I would probably communicate more with my guild from the beginning (we didn't start a group chat until well after Thanksgiving break).
# Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
#* Content: What is the quality of the work?
#** I think that my team's portion of GRNsight Gene Page Project and Group Report is very high quality.
#* Organization: Comment on the organization of the project and of your group's wiki pages.
#* Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Emma's Individual Statement

2017-12-14T05:28:22Z

Emmatyrnauer: /* Statement of Work */ typo

Emma's Individual Statement

2017-12-14T05:27:46Z

Emmatyrnauer: /* Statement of Work */ completing statement

Emma's Individual Statement

2017-12-14T04:58:08Z

Emmatyrnauer: /* Statement of Work */ adding progress with links

Emma's Individual Statement

2017-12-14T04:31:30Z

Emmatyrnauer: /* Individual Assessment and Reflection */ rearranging

==Individual Assessment and Reflection==
===Statement of Work===
# Describe exactly what you did on the project.
# Provide references or links to artifacts of your work, such as:

===Assessment of Project===
#Give an objective assessment of the success of your project workflow and teamwork.
#* What worked and what didn't work?
#* What would you do differently if you could do it all over again?
# Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas===
#* Content: What is the quality of the work?
#* Organization: Comment on the organization of the project and of your group's wiki pages.
#* Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Emma's Individual Statement

2017-12-14T04:30:36Z

Emmatyrnauer: creating outline of page

==Individual Assessment and Reflection==
===Statement of Work===
# Describe exactly what you did on the project.
# Provide references or links to artifacts of your work, such as:

===Assessment of Project===
#Give an objective assessment of the success of your project workflow and teamwork.
#* What worked and what didn't work?
#* What would you do differently if you could do it all over again?

===Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas===
# Content: What is the quality of the work?
# Organization: Comment on the organization of the project and of your group's wiki pages.
# Completeness: Did your team achieve all of the project objectives? Why or why not?

===Reflection on the Process===
# What did you learn?
# With your head (biological or computer science principles)
# With your heart (personal qualities and teamwork qualities that make things work or not work)?
# With your hands (technical skills)?
# What lesson will you take away from this project that you will still use a year from now?

Lights, Camera, InterACTION! Deliverables

2017-12-14T04:27:57Z

Emmatyrnauer: /* Individual Statements */ adding emma individual statement page

===Group Report and Presentation===
Presentation: [[Media:LCI Presentation.pdf]]

===Individual Statements===
[[Emma's Individual Statement]]

===Code and README===

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:GRNsight_inputoutput_excelandimages.zip]]‎
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

File:LCI Presentation.pdf

2017-12-12T21:04:23Z

Emmatyrnauer: Emmatyrnauer uploaded a new version of File:LCI Presentation.pdf

Emmatyrnauer Week 15

2017-12-12T05:00:08Z

Emmatyrnauer: creating final individual page

==Electronic Notebook==

==Acknowledgements==
#[[Lights, Camera, InterACTION!]] for collaboration in the creation of the group presentation and paper.
# Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
# Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
# Matlab for creating the output file which was used to create weighted gene regulation map.
# GRNsight for generation of gene map (both weighted and unweighted).
# While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

==References==
#Yeastract
#Matlab
GRNsight

{{Emmatyrnauer}}

File:GRNsight inputoutput excelandimages.zip

2017-12-10T05:32:28Z

Emmatyrnauer: Emmatyrnauer uploaded a new version of File:GRNsight inputoutput excelandimages.zip

final

Lights, Camera, InterACTION! Deliverables

2017-12-10T05:23:58Z

Emmatyrnauer: /* GRNmap input and output workbooks */ typo

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:GRNsight_inputoutput_excelandimages.zip]]‎
# Individual gene .jpg's from matlab output: [[Media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Lights, Camera, InterACTION! Deliverables

2017-12-10T05:23:27Z

Emmatyrnauer: /* GRNmap input and output workbooks */

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:GRNsight_inputoutput_excelandimages.zip]]‎
# Individual gene .jpg's from matlab output: [[media:Emmat_gene_jpg_matlab.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

File:Emmat gene jpg matlab.zip

2017-12-10T05:22:42Z

Emmatyrnauer: individual jpgs for genes

individual jpgs for genes

Lights, Camera, InterACTION! Deliverables

2017-12-10T05:18:14Z

Emmatyrnauer: adding links

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results, gene list and GO list files===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]
# Powerpoint presentation with stem images (also linked below under GRNmap workbooks): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:GRNsight_inputoutput_excelandimages.zip]]‎

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Lights, Camera, InterACTION! Deliverables

2017-12-10T05:12:36Z

Emmatyrnauer: /* GRNmap input and output workbooks */ changed file name

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]

===Gene List and GO list files===

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:GRNsight_inputoutput_excelandimages.zip]]‎

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

File:GRNsight inputoutput excelandimages.zip

2017-12-10T05:11:41Z

Emmatyrnauer: final

final

Lights, Camera, InterACTION! Deliverables

2017-12-10T05:08:23Z

Emmatyrnauer: /* GRNmap input and output workbooks */ typo

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]

===Gene List and GO list files===

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:Emmat_GRNmap_inputoutput_excel_and_images.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Lights, Camera, InterACTION! Deliverables

2017-12-10T05:07:11Z

Emmatyrnauer: /* GRNmap input and output workbooks */ adding final workbook

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]

===Gene List and GO list files===

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]
# Final excel workbooks and GRNmap images after Matlab utilized: [[Media:Emmat_GRNmap_inputoutput_excel__and_images.zip]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Lights, Camera, InterACTION! Deliverables

2017-12-10T04:55:35Z

Emmatyrnauer: /* Electronic notebook corresponding to microarray results */ adding other electronic notebooks

===Group Report and Presentation===
Draft of presentation: [[Media:Draft_LCI_Final_Presentation.pdf]]

===Individual Statements===

===Code and README===

===ANOVA and stem results===
# Excel workbook: [[Media:Wt_Microarraydata_ET.zip]]
# File used to run stem, gene list tables, GO list tables: [[Media:Week10_filesforstem_wildtype_emmat.zip‎]]

===Gene List and GO list files===

===YEASTRACT results===
# YEASTRACT rank by TF results: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]]

===GRNmap input and output workbooks===
# Input: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
# Output (within powerpoint presentation): [[Media:Wt_profileimage_presentation_emmat.pptx]]

===Electronic notebook corresponding to microarray results===
# [[Emmatyrnauer Week 8]]
# [[Emmatyrnauer Week 10]]
# [[Emmatyrnauer Week 11]]
# [[Emmatyrnauer Week 12]]
# [[Emmatyrnauer Week 14]]
# [[Emmatyrnauer Week 15]]
{{template:Pugs Not Drugs}}

Emmatyrnauer Week 14

2017-12-05T23:54:52Z

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ specification

==Electronic notebook for the continuation of Week 10 Data Analysis==
=== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ===

In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time. The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors. I explored this using the YEASTRACT database.

# I opened the gene list in Excel for the one of the significant profiles from my stem analysis (profile 45). I chose this cluster because it has a clear cold shock/recovery up/down pattern. It is also a large cluster.
#* I copied the list of gene IDs from my clipboard (C6:C585).
# I launched a web browser and went to the [http://www.yeastract.com/ YEASTRACT database].
#* On the left panel of the window, I clicked on the link to [http://www.yeastract.com/formrankbytf.php ''Rank by TF''].
#* I pasted the list of genes from the cluster (profile 45) into the box labeled ''ORFs/Genes''.
#* I checked the box for ''Check for all TFs''.
#* I accepted the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
#* I did '''''not''''' apply a filter for "Filter Documented Regulations by environmental condition".
#* I ranked genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
#* I clicked the ''Search'' button.
# I answered the following questions:
#* In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant". '''''How many transcription factors are green or "significant"?'''''
#**'''23 transcription factors are green/significant'''
#* '''''I copied the table of results from the web page and pasted it into a new Excel workbook to preserve the results.'''''
#** '''''I uploaded the Excel file to wiki linked to it here: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]].'''''
#** '''''Is your transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".''''' (Note: I didn't answer this because I was assigned the wt strain).
# For the mathematical model and GRNsight, I needed to define a ''gene regulatory network'' of transcription factors that regulatde other transcription factors. I used YEASTRACT to assist me with creating the network. I wanted to generate a network with approximately 15-30 transcription factors in it.
#* I selected from this list of "significant" transcription factors, which ones I was going to use to run the model. I used these transcription factors and added GLN3 because it was not already in my list. Justification: I chose all of the significant transcription factors from profile 45 because there were less than 30 and this would provide extra transcription factors for the network just in case some did not have connections to any of the others. List of transcription factors: ACE2, ARG80, GAT3, GCR2, GLN3, HAP4, INO4, MIG2, MSN2, NDT80, PDR3, SFP1, STB5, SUT1, UME6, YAP1, YHP1, YLR278C, and YOX1
#* I went back to the YEASTRACT database and followed the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''.
#* I copied and pasted the list of transcription factors I identified into both the "Transcription factors" field and the "Target ORF/Genes" field. I had to delete the spaces before each of the names for the regulatory network to generate properly.
#* I used the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"
#** I clicked the "Generate" button.
#** In the results window that appeared, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop. I renamed this file to "RegulationMatrix_yeastract_week10etf"


=== Visualizing My Gene Regulatory Network with GRNsight===

I analyzed the regulatory matrix file I generated above in Microsoft Excel and visualized it using GRNsight.
# First I needed to properly format the output file from YEASTRACT.
#* I opened the file in Excel. It did not open properly in Excel because a semicolon was used as the column delimiter instead of a comma. To fix this, I selected the entire Column A. I then went to the "Data" tab and selected "Text to columns". In the Wizard that appeared, I selected "Delimited" and clicked "Next". In the next window, I selected "Semicolon", and clicked "Next". In the next window, I left the data format at "General", and clicked "Finish". This now looked like a table with the names of the transcription factors across the top and down the first column and all of the zeros and ones distributed throughout the rows and columns. This is called an "adjacency matrix." If there is a "1" in the cell, that means there is a connection between the trancription factor in that row with that column.
#* I saved this file in Microsoft Excel workbook format (.xlsx).
#* I checked to see that all of the transcription factors in the matrix were connected to at least one of the other transcription factors by making sure that there was at least one "1" in a row or column for that transcription factor. If a factor was not connected to any other factor, I deleted its row and column from the matrix ( RIM101 and ASG1 were deleted). I made sure that I still had somewhere between 15 and 30 transcription factors in my network after this pruning (19).
#** I only deleted the transcription factor if there were all zeros in its column '''AND''' all zeros in its row.
#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), I needed to transpose the matrix. I inserted a new worksheet into my Excel file and named it "network". I went back to the previous sheet and selected the entire matrix and copied it. I went to my new worksheet and clickeded on the A1 cell in the upper left. I selected "Paste special" from the "Home" tab. In the window that appeared, I checked the box for "Transpose". This pasted my data with the columns transposed to rows and vice versa. This is necessary because I wanteded the transcription factors that were the "regulatORS" across the top and the "regulatEES" along the side.
#* The labels for the genes in the columns and rows needed to match. Thus, I deleted the "p" from each of the gene names in the columns. I also adjusted the case of the labels to make them all upper case.
#* In cell A1, I copied and pasted the text "rows genes affected/cols genes controlling".
#* Finally, for ease of working with the adjacency matrix in Excel, I wanted to alphabetize the gene labels both across the top and side.
#** I selected the area of the entire adjacency matrix.
#** I clicked the Data tab and clicked the custom sort button.
#** I sorted Column A alphabetically, being sure to exclude the header row.
#** I then sorted row 1 from left to right, excluding cell A1. In the Custom Sort window, I clicked on the options button and selected sort left to right, excluding column 1.
#* I named the worksheet containing my organized adjacency matrix "network" and Saved.
#**File: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
#**File after edits during class (#5 is the final version): [[Media: REGULATIONMATRIXFINAL_ET.zip]]
# Now I visualized what these gene regulatory networks look like with the GRNsight software.
#* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network. I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results. I pasted it into my PowerPoint presentation from week 10 and uploaded a new version of the powerpoint including this screenshot to wiki: [[Media:Wt_profileimage_presentation_emmat.pptx]]

====Conclusion====
For the assignment this week, I used the YEASTRACT database to determine the connection between the regulation of different genes from the profile 45 genelist of the wild type microarray data. Yeastract allowed me to identify similarities in the expression pattern (through transcription factors) of the different genes. From profile 45, 23 transcription factors were identified as significant (these transcription factors regulated the most genes in the genelist of profile 45). I then used YEASTRACT to generate a regulation matrix of the 23 transcription factors--i also added GLN3 per the instructions. Finally, I made some adjustments to this regulation matrix (which was downloaded as a CSV file) to allow for it to be readable by GRNsight. I opened it in GRNsight which generated a graph of my network. This network graphically depicted the connections between the different genes.

==Acknowledgements==
#Dr. Dahlquist for teaching and assisting me with the data analysis
#The data analyst guild for assisting with the data analysis
# I copied and modified the instructions from the [[Week 10]] assignment page.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:38, 4 December 2017 (PST)

==References==
#LMU BioDB 2017. (2017). Week 10. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#YEASTRACT. Retrieved December 4, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
# GRNsight (2017) Retrieved December 4, 2017, from http://dondi.github.io/GRNsight/
{{Emmatyrnauer}}

Emmatyrnauer Week 14

2017-12-05T23:54:04Z

Emmatyrnauer: /* Visualizing My Gene Regulatory Network with GRNsight */ editing excel workbook

==Electronic notebook for the continuation of Week 10 Data Analysis==
=== Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes ===

In the previous analysis using STEM, we found a number of gene expression profiles (aka clusters) which grouped genes based on similarity of gene expression changes over time. The implication is that these genes share the same expression pattern because they are regulated by the same (or the same set) of transcription factors. I explored this using the YEASTRACT database.

# I opened the gene list in Excel for the one of the significant profiles from my stem analysis (profile 45). I chose this cluster because it has a clear cold shock/recovery up/down pattern. It is also a large cluster.
#* I copied the list of gene IDs from my clipboard (C6:C585).
# I launched a web browser and went to the [http://www.yeastract.com/ YEASTRACT database].
#* On the left panel of the window, I clicked on the link to [http://www.yeastract.com/formrankbytf.php ''Rank by TF''].
#* I pasted the list of genes from the cluster (profile 45) into the box labeled ''ORFs/Genes''.
#* I checked the box for ''Check for all TFs''.
#* I accepted the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
#* I did '''''not''''' apply a filter for "Filter Documented Regulations by environmental condition".
#* I ranked genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
#* I clicked the ''Search'' button.
# I answered the following questions:
#* In the results window that appears, the p values colored green are considered "significant", the ones colored yellow are considered "borderline significant" and the ones colored pink are considered "not significant". '''''How many transcription factors are green or "significant"?'''''
#**'''23 transcription factors are green/significant'''
#* '''''I copied the table of results from the web page and pasted it into a new Excel workbook to preserve the results.'''''
#** '''''I uploaded the Excel file to wiki linked to it here: [[Media:Yeastract_profile45results_preserved_emmat.xlsx]].'''''
#** '''''Is your transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".''''' (Note: I didn't answer this because I was assigned the wt strain).
# For the mathematical model and GRNsight, I needed to define a ''gene regulatory network'' of transcription factors that regulatde other transcription factors. I used YEASTRACT to assist me with creating the network. I wanted to generate a network with approximately 15-30 transcription factors in it.
#* I selected from this list of "significant" transcription factors, which ones I was going to use to run the model. I used these transcription factors and added GLN3 because it was not already in my list. Justification: I chose all of the significant transcription factors from profile 45 because there were less than 30 and this would provide extra transcription factors for the network just in case some did not have connections to any of the others. List of transcription factors: ACE2, ARG80, GAT3, GCR2, GLN3, HAP4, INO4, MIG2, MSN2, NDT80, PDR3, SFP1, STB5, SUT1, UME6, YAP1, YHP1, YLR278C, and YOX1
#* I went back to the YEASTRACT database and followed the link to ''[http://www.yeastract.com/formgenerateregulationmatrix.php Generate Regulation Matrix]''.
#* I copied and pasted the list of transcription factors I identified into both the "Transcription factors" field and the "Target ORF/Genes" field. I had to delete the spaces before each of the names for the regulatory network to generate properly.
#* I used the "Regulations Filter" options of "Documented", "'''Only''' DNA binding evidence"
#** I clicked the "Generate" button.
#** In the results window that appeared, I clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop. I renamed this file to "RegulationMatrix_yeastract_week10etf"


=== Visualizing My Gene Regulatory Network with GRNsight===

I analyzed the regulatory matrix file I generated above in Microsoft Excel and visualized it using GRNsight.
# First I needed to properly format the output file from YEASTRACT.
#* I opened the file in Excel. It did not open properly in Excel because a semicolon was used as the column delimiter instead of a comma. To fix this, I selected the entire Column A. I then went to the "Data" tab and selected "Text to columns". In the Wizard that appeared, I selected "Delimited" and clicked "Next". In the next window, I selected "Semicolon", and clicked "Next". In the next window, I left the data format at "General", and clicked "Finish". This now looked like a table with the names of the transcription factors across the top and down the first column and all of the zeros and ones distributed throughout the rows and columns. This is called an "adjacency matrix." If there is a "1" in the cell, that means there is a connection between the trancription factor in that row with that column.
#* I saved this file in Microsoft Excel workbook format (.xlsx).
#* I checked to see that all of the transcription factors in the matrix were connected to at least one of the other transcription factors by making sure that there was at least one "1" in a row or column for that transcription factor. If a factor was not connected to any other factor, I deleted its row and column from the matrix ( RIM101 and ASG1 were deleted). I made sure that I still had somewhere between 15 and 30 transcription factors in my network after this pruning (19).
#** I only deleted the transcription factor if there were all zeros in its column '''AND''' all zeros in its row.
#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), I needed to transpose the matrix. I inserted a new worksheet into my Excel file and named it "network". I went back to the previous sheet and selected the entire matrix and copied it. I went to my new worksheet and clickeded on the A1 cell in the upper left. I selected "Paste special" from the "Home" tab. In the window that appeared, I checked the box for "Transpose". This pasted my data with the columns transposed to rows and vice versa. This is necessary because I wanteded the transcription factors that were the "regulatORS" across the top and the "regulatEES" along the side.
#* The labels for the genes in the columns and rows needed to match. Thus, I deleted the "p" from each of the gene names in the columns. I also adjusted the case of the labels to make them all upper case.
#* In cell A1, I copied and pasted the text "rows genes affected/cols genes controlling".
#* Finally, for ease of working with the adjacency matrix in Excel, I wanted to alphabetize the gene labels both across the top and side.
#** I selected the area of the entire adjacency matrix.
#** I clicked the Data tab and clicked the custom sort button.
#** I sorted Column A alphabetically, being sure to exclude the header row.
#** I then sorted row 1 from left to right, excluding cell A1. In the Custom Sort window, I clicked on the options button and selected sort left to right, excluding column 1.
#* I named the worksheet containing my organized adjacency matrix "network" and Saved.
#**File: [[Media:RegulationMatrix_yeastract_week10etf.xlsx]]
#**File after edits during class: [[Media: REGULATIONMATRIXFINAL_ET.zip]]
# Now I visualized what these gene regulatory networks look like with the GRNsight software.
#* I went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* I selected the menu item File > Open and selected the regulation matrix .xlsx file that had the "network" worksheet in it that I formatted above. GRNsight automatically created a graph of my network. I moved the nodes (genes) around until you got a layout that I liked and took a screenshot of the results. I pasted it into my PowerPoint presentation from week 10 and uploaded a new version of the powerpoint including this screenshot to wiki: [[Media:Wt_profileimage_presentation_emmat.pptx]]

====Conclusion====
For the assignment this week, I used the YEASTRACT database to determine the connection between the regulation of different genes from the profile 45 genelist of the wild type microarray data. Yeastract allowed me to identify similarities in the expression pattern (through transcription factors) of the different genes. From profile 45, 23 transcription factors were identified as significant (these transcription factors regulated the most genes in the genelist of profile 45). I then used YEASTRACT to generate a regulation matrix of the 23 transcription factors--i also added GLN3 per the instructions. Finally, I made some adjustments to this regulation matrix (which was downloaded as a CSV file) to allow for it to be readable by GRNsight. I opened it in GRNsight which generated a graph of my network. This network graphically depicted the connections between the different genes.

==Acknowledgements==
#Dr. Dahlquist for teaching and assisting me with the data analysis
#The data analyst guild for assisting with the data analysis
# I copied and modified the instructions from the [[Week 10]] assignment page.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 19:38, 4 December 2017 (PST)

==References==
#LMU BioDB 2017. (2017). Week 10. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#YEASTRACT. Retrieved December 4, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
# GRNsight (2017) Retrieved December 4, 2017, from http://dondi.github.io/GRNsight/
{{Emmatyrnauer}}

File:REGULATIONMATRIXFINAL ET.zip

2017-12-05T23:52:55Z

Emmatyrnauer: edits during class

edits during class