Difference between revisions of "Aporras1 Week 14"

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=== Visualizing Your Gene Regulatory Networks with GRNsight===
 
=== Visualizing Your Gene Regulatory Networks with GRNsight===
 +
#* Opened the file, [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]], in Excel.
 +
#* Fixed formatting:
 +
#** Selected the entire Column A.  Then went to the "Data" tab and selected "Text to columns". In the Wizard that appears, selected "Delimited" and clicked "Next".  In the next window, selected "Semicolon", and clicked "Next".  In the next window, left the data format at "General", and clicked "Finish".
 +
#** Known as 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.
 +
#* Saved this file in Microsoft Excel workbook format (.xlsx).
 +
#** YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
 +
#* Checked to see that all of the transcription factors in the matrix are 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.
 +
#** No transcription factors were deleted as all had at least "1" in a row or column for that transcription factor.
 +
#* Inserted a new worksheet into the Excel file, [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]. and named it "network".  Went back to the previous sheet and selected the entire matrix and copied it. Went to the new worksheet and clicked on the A1 cell in the upper left.  Selected "Paste special" from the "Home" tab.  In the window that appears, checked the box for "Transpose".
 +
#* Deleted the "p" from each of the gene names in the columns.  Adjusted the case of the labels to make them all upper case.
 +
#* In cell A1, copied and pasted the text "rows genes affected/cols genes controlling".
 +
#* Alphabetization:
 +
#** Selected the area of the entire adjacency matrix.
 +
#** Clicked the Data tab and clicked the custom sort button.
 +
#** Sorted Column A alphabetically, excluding the header row.
 +
#** Sorted row 1 from left to right, excluding cell A1.  In the Custom Sort window, clicked on the options button and select sort left to right, excluding column 1.
 +
#* Named the worksheet containing your organized adjacency matrix "network" and Save.
 +
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
 +
#* Selected the menu item File > Open and selected "[[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked and took a screenshot of the results and saved the screenshot as "[[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]"
  
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We will analyze the regulatory matrix files you generated above in Microsoft Excel and visualize them using GRNsight to determine which one will be appropriate to pursue further in the modeling.
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== Summary Paragraph ==
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# First we need to properly format the output files from YEASTRACT.  You will repeat these steps for each of the three files you generated above.
+
For [[Week 14|Week 14]], I was assigned the task of making edits to [[Week 8|Week 8]] and [[Week 10|Week 10]] along with completing the remaining parts of [[Week 10|Week 10]]. First, I selected the profile22 genelist and ranked the transcription factors using YEASTRACT and found that 49 of the transcription factors were significant.  I further ranked those transcription factors  from the lowest p-value to the highest p-value and chose the 20 lowest p-values. Two other transcription factors, HAP4 and GLN3 were including per instructions. These selected transcription factors listed above were put into the YEASTRACT database to generate a regulation matrix. This regulation matrix was then used to create a regulation network from GRNsight to visualize the regulation between these transcription factors. This proves extremely helpful as a method of visualization the connections and ways that the transcription factors interact and regulate each other and even regulate themselves.
−
#*  Open the file in Excel.  It will not open properly in Excel because a semicolon was used as the column delimiter instead of a comma.  To fix this, Select the entire Column A.  Then go to the "Data" tab and select "Text to columns".  In the Wizard that appears, select "Delimited" and click "Next". In the next window, select "Semicolon", and click "Next".  In the next window, leave the data format at "General", and click "Finish".  This should now look 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.
 
−
#* Save this file in Microsoft Excel workbook format (.xlsx).
 
−
#* Check to see that all of the transcription factors in the matrix are connected to at least one of the other transcription factors by making sure that there is at least one "1" in a row or column for that transcription factor.  If a factor is not connected to any other factor, delete its row and column from the matrix.  Make sure that you still have somewhere between 15 and 30 transcription factors in your network after this pruning.
 
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#** Only delete the transcription factor if there are all zeros in its column '''AND''' all zeros in its row. You may find visualizing the matrix in GRNsight (below) can help you find these easily.
 
−
#* For this adjacency matrix to be usable in GRNmap (the modeling software) and GRNsight (the visualization software), we need to transpose the matrix. Insert a new worksheet into your Excel file and name it "network".  Go back to the previous sheet and select the entire matrix and copy it.  Go to you new worksheet and click on the A1 cell in the upper left.  Select "Paste special" from the "Home" tab.  In the window that appears, check the box for "Transpose".  This will paste your data with the columns transposed to rows and vice versa. This is necessary because we want the transcription factors that are the "regulatORS" across the top and the "regulatEES" along the side.
 
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#* The labels for the genes in the columns and rows need to match. Thus, delete the "p" from each of the gene names in the columns.  Adjust the case of the labels to make them all upper case.
 
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#* In cell A1, copy and paste the text "rows genes affected/cols genes controlling".
 
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#* Finally, for ease of working with the adjacency matrix in Excel, we want to alphabatize the gene labels both across the top and side.
 
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#** Select the area of the entire adjacency matrix.
 
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#** Click the Data tab and click the custom sort button.
 
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#** Sort Column A alphabetically, being sure to exclude the header row.
 
−
#** Now sort row 1 from left to right, excluding cell A1.  In the Custom Sort window, click on the options button and select sort left to right, excluding column 1.
 
−
#* Name the worksheet containing your organized adjacency matrix "network" and Save.
 
−
# Now we will visualize what these gene regulatory networks look like with the GRNsight software.
 
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#* Go to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
 
−
#* Select the menu item File > Open and select the regulation matrix .xlsx file that has the "network" worksheet in it that you formatted above.  If the file has been formatted properly, GRNsight should automatically create a graph of your network.  Move the nodes (genes) around until you get a layout that you like and take a screenshot of the results.  Paste it into your PowerPoint presentation.
 
  
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==== Summary of what you need to turn in for the individual Week 10 assignment ====
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== Deliverables ==
−
 
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# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
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# Your individual journal page should have an '''''electronic lab notebook''''' recording your work.  This includes the detailed methods specific to your analysis, your result files, the answers to any questions posed in the protocol above, a scientific conclusion, and the acknowledgments and references sections.  Don't forget your paragraph which is a biological interpretation of your stem results.
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# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
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# Upload your updated Excel spreadsheet to the wiki that has today's manipulations in it.  Use the same filename as before so that the download link that you already (previous versions will still be available in the history).
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# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
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# Append the screenshots of the stem results to the PowerPoint presentation that contains the p value table that you created for the [[Week 8]] assignments.  Each slide in the presentation should have a meaningful title that describes the main message of the slide.
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# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
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# Zip together all of the tab-delimited text files that you created for and from stem and upload them to the wiki.
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# Screenshot of GRNsight Regulatory Network: [[File:AP Regulation Matrix profile22 GRNsight Network.PNG|900px|File:900pixels]]
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#* the file that was saved from your original spreadsheet that you used to run stem
 
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#* each of the genelist and GOlist files for each of your significant profiles.
 
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# Write a paragraph-length conclusion for this week's exercise.
 
−
 
 
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===Deliverables===
 
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# [[Media:AP YEASTRACT Transcription Factors.xlsx]]
 
−
# [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
 
  
 
==Acknowledgements==
 
==Acknowledgements==
−
#Recieved help from both [[User:Dondi|Dondi]] and [[User:Kdahlquist|Dr. Dahlquist]] from feedback given and instructions given in class.
+
# Recieved help from both [[User:Dondi|Dondi]] and [[User:Kdahlquist|Dr. Dahlquist]] from feedback given and instructions given in class.
−
#Copied and modified the instructions from [[Week 10|Week 10]].
+
# Copied and modified the instructions from [[Week 10|Week 10]].
 +
# Texted the data analyst group chat for questions including: [[User:Mbalducc|Mary Balducci]], [[User:dbashour|Dina Bashoura]], and [[User:Emmatyrnauer|Emma Tyrnauer]].
  
 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
Line 125: Line 122:
  
 
==References==
 
==References==
 +
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
 
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
 
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
 
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
 +
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
  
 
[[Category:Journal Entry]]
 
[[Category:Journal Entry]]

Latest revision as of 01:47, 4 December 2017

User page: Antonio Porras

Team page: JASPAR The Friendly Ghost

Assignment page: Week 14

Electronic Lab Notebook

Edits to Week 8 & 10

Made edits in the Week 8 and Week 10 electronic notebooks and journal entries in accordance to the feedback given from Dr. Dahlquist and Dr. Dionisio.

  • Edits to: Week 8
    • Provided exact formulas used in excel.
    • Made sure tense was consistent throughout the electronic notebook.
    • Corrected powerpoint provided by supplying correct values.
    • Extended concluding paragraph.
    • Acknowledged source of data and specified acknowledgements.
  • Edits to: Week 10
    • Included specific filenames.
    • Reported definitions for 6 GO terms.
      • Interpreted GO terms in terms of cold shock.
    • Updated references to include GO term definitions.
    • Updated acknowledgements to specify instructions were copied and modified from Week 10 assignment page.
    • Included the excel file used for the stem.
    • Included the .txt file that was used for the stem.
    • Added summary paragraph to the end of the journal entry.

Using YEASTRACT to Infer which Transcription Factors Regulate a Cluster of Genes

  1. Opened the gene list in Excel for profile 22 from my stem analysis.
  2. Launched a web browser and went to the YEASTRACT database.
    • On the left panel of the window, clicked on the link to Rank by TF.
    • Pasted the list of genes from profile 22 into the box labeled ORFs/Genes.
    • Checked the box for Check for all TFs.
    • Accepted the defaults for the Regulations Filter (Documented, DNA binding plus expression evidence)
    • Did not apply a filter for "Filter Documented Regulations by environmental condition".
    • Ranked genes by TF using: The % of genes in the list and in YEASTRACT regulated by each TF.
    • Clicked the Search button.
  3. Questions:
    • How many transcription factors are green or "significant"?
      • 49 transcription factors are green or significant.
      • 13 transcription factors are yellow or borderline significant.
      • 125 transcription factors are pink or insignificant.
    • Copied the table of results from the web page and pasted it into a new Excel workbook.
    • Is dZAP1 transcription factor on the list? If so, what is their "% in user set", "% in YEASTRACT", and "p value".
      • dZAP1p is on the list.
        • 43.03% in user set
        • 7.02% in YEASTRACT
        • p-value: 2E-15
    • Chose the listed transcription factors from the 49 "significant" TFs and selected 20 with the highest value of "% in user set" because they target a high percentage of the genes within my dataset. Also included two transcription factors, GLN3 & HAP4 as directed by the Week 10 instructions. List of "significant" transcription factors used to run the model:
      • GLN3
      • HAP4
      • Ace2p
      • Sfp1p
      • Bas1p
      • Msn2p
      • Yap1p
      • Ash1p
      • Gcn4p
      • Msn4p
      • Abf1p
      • Cst6p
      • Sok2p
      • Rpn4p
      • Hsf1p
      • Zap1p
      • Cin5p
      • Aft1p
      • Spt23p
      • Pdr1p
      • Met4p
      • Arr1p
    • Went back to the YEASTRACT database and followed the link to Generate Regulation Matrix.
    • Copied and pasted the list of transcription factors I identified above into both the "Transcription factors" field and the "Target ORF/Genes" field.
    • Used the "Regulations Filter" options of "Documented", "Only DNA binding evidence"
      • Clicked the "Generate" button.
      • In the results window that appeared, clicked on the link to the "Regulation matrix (Semicolon Separated Values (CSV) file)" that appeared and saved it to my Desktop.

Visualizing Your Gene Regulatory Networks with GRNsight

    • Opened the file, Media:AP Regulation Matrix profile22 dZAP1.xlsx, in Excel.
    • Fixed formatting:
      • Selected the entire Column A. Then went to the "Data" tab and selected "Text to columns". In the Wizard that appears, selected "Delimited" and clicked "Next". In the next window, selected "Semicolon", and clicked "Next". In the next window, left the data format at "General", and clicked "Finish".
      • Known as 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.
    • Saved this file in Microsoft Excel workbook format (.xlsx).
    • Checked to see that all of the transcription factors in the matrix are 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.
      • No transcription factors were deleted as all had at least "1" in a row or column for that transcription factor.
    • Inserted a new worksheet into the Excel file, Media:AP Adjacency Matrix profile22 dZAP1.xlsx. and named it "network". Went back to the previous sheet and selected the entire matrix and copied it. Went to the new worksheet and clicked on the A1 cell in the upper left. Selected "Paste special" from the "Home" tab. In the window that appears, checked the box for "Transpose".
    • Deleted the "p" from each of the gene names in the columns. Adjusted the case of the labels to make them all upper case.
    • In cell A1, copied and pasted the text "rows genes affected/cols genes controlling".
    • Alphabetization:
      • Selected the area of the entire adjacency matrix.
      • Clicked the Data tab and clicked the custom sort button.
      • Sorted Column A alphabetically, excluding the header row.
      • Sorted row 1 from left to right, excluding cell A1. In the Custom Sort window, clicked on the options button and select sort left to right, excluding column 1.
    • Named the worksheet containing your organized adjacency matrix "network" and Save.
  2. Went to the GRNsight home page.

Summary Paragraph

For Week 14, I was assigned the task of making edits to Week 8 and Week 10 along with completing the remaining parts of Week 10. First, I selected the profile22 genelist and ranked the transcription factors using YEASTRACT and found that 49 of the transcription factors were significant. I further ranked those transcription factors from the lowest p-value to the highest p-value and chose the 20 lowest p-values. Two other transcription factors, HAP4 and GLN3 were including per instructions. These selected transcription factors listed above were put into the YEASTRACT database to generate a regulation matrix. This regulation matrix was then used to create a regulation network from GRNsight to visualize the regulation between these transcription factors. This proves extremely helpful as a method of visualization the connections and ways that the transcription factors interact and regulate each other and even regulate themselves.

Deliverables

  1. YEASTRACT Transcription Factor Data: Media:AP YEASTRACT Transcription Factors.xlsx
  2. YEASTRACT Regulation Matrix Profile: Media:AP Regulation Matrix profile22 dZAP1.xlsx
  3. YEASTRACT Adjacency Matrix: Media:AP Adjacency Matrix profile22 dZAP1.xlsx
  4. YEASTRACT Adjacency Matrix with Network for GRNsight: Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx
  5. Screenshot of GRNsight Regulatory Network: File:900pixels

Acknowledgements

  1. Recieved help from both Dondi and Dr. Dahlquist from feedback given and instructions given in class.
  2. Copied and modified the instructions from Week 10.
  3. Texted the data analyst group chat for questions including: Mary Balducci, Dina Bashoura, and Emma Tyrnauer.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Aporras1 (talk) 16:53, 28 November 2017 (PST)

References

  1. Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
  2. LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
  3. LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
  4. LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
  5. Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
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