Difference between revisions of "Ckaplan Week 10"
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I adjusted optimization parameters as instructed. | I adjusted optimization parameters as instructed. | ||
I saved and uploaded the Excel Workbook to the wiki. | I saved and uploaded the Excel Workbook to the wiki. | ||
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| + | Creating and Visualizing My Gene Regulatory Network with GRNsight: | ||
| + | From profile 45, I selected transcription factors from the list of significant ones in YEASTRACT to build a gene regulatory network using GRNsight. I ensured that the network had approximately 15-20 connected transcription factors and exported the network image as a PNG file, uploading it to the wiki and displaying it on my individual journal page. | ||
===Methods/Results:=== | ===Methods/Results:=== | ||
Revision as of 19:09, 31 March 2024
Contents
Purpose:
This assignment helps us learn microarray data analysis and gene analysis techniques. It also provides practice in determining p-values and organizing data effectively.
Procedure:
Prepare Microarray Data for STEM: I created a new worksheet named "dGln3_stem" in Excel. I copied data from the "dGln3_ANOVA" worksheet and pasted values into "dGln3_stem". I renamed columns: "Master_Index" to "SPOT", "ID" to "Gene Symbol", and deleted the column "Standard_Name". I filtered data on the B-H corrected p value (> 0.05), deleted irrelevant rows, and retained only significant gene expression changes. I deleted unnecessary columns, leaving only Average Log Fold Change columns for each time point and renamed them. I removed #DIV/0! errors. I saved the spreadsheet as Text (Tab-delimited) (*.txt) after turning on file extensions.
Setting up STEM: I downloaded and extracted the STEM software. I downloaded the Gene Ontology and yeast GO annotations files and placed them in the STEM folder. I launched STEM by double-clicking on stem.jar. In the main STEM interface, I configured settings in sections 1 to 4 as instructed. I ran STEM by clicking the Execute button. Viewing and Saving STEM Results: I reviewed the generated STEM Profiles. I adjusted the X-axis scale to "Based on real time". I took screenshots of significant profiles and saved them in a PowerPoint presentation. I saved gene lists and GO term lists for significant profiles as instructed. Analyzing STEM Results: I chose a significant profile with a clear cold shock/recovery pattern. I examined the number of genes belonging to the profile and the p value for enrichment of genes. I filtered GO terms based on p values and selected 6 significant terms for further analysis. I looked up definitions of selected GO terms on the Gene Ontology website.
Using YEASTRACT: I copied gene IDs from the chosen profile in Excel. I visited the YEASTRACT database and pasted the gene list. I ranked genes by TF and noted significant transcription factors. Creating and Visualizing Gene Regulatory Network with GRNsight: I selected transcription factors from YEASTRACT results, including GLN3. I loaded the network in GRNsight, ensuring connectivity. I recorded the number of genes and edges. I exported the network image as a PNG and uploaded it to the wiki. Creating GRNmap Input Workbook: I exported data from GRNsight to Excel. I checked sheets for correctness, ensuring adjacency matrix, log2 fold changes, and other parameters. I inserted a new worksheet named "network_weights" and copied the network data. I adjusted optimization parameters as instructed. I saved and uploaded the Excel Workbook to the wiki.
Creating and Visualizing My Gene Regulatory Network with GRNsight: From profile 45, I selected transcription factors from the list of significant ones in YEASTRACT to build a gene regulatory network using GRNsight. I ensured that the network had approximately 15-20 connected transcription factors and exported the network image as a PNG file, uploading it to the wiki and displaying it on my individual journal page.
Methods/Results:
Media: BIOL367_S24_microarray-data_dGLN3CKAS31211.xlsx
Media:Updated_Pvalues_ckaplan.pdf
Media:Andrew&Charlotte_Tables_Gene-GoData.zip
Media:AS&CK_BIOL367_S24_STEM_PHOTOS_dGLN3.pptx
Media:Yeastract_45_Gene_CK.xlsx
Media:GRN_(Yeastmine_-_SGD__2024-03-19;_13_genes,_21_edges)_weighted_(2)_ck_45.xlsx
- Why did you select this profile? In other words, why was it interesting to you?
I selected profile 45 because I thought it was interesting because out of all off our profiles, it had the most genes.
- How many genes belong to this profile?
406
- How many genes were expected to belong to this profile?
29.9
- What is the p value for the enrichment of genes in this profile?
0.00
I have 44 green genes
Gln3p 46.65% Cin5p 31.27%
Acknowledgments
I worked with Andrew in and out of class throughout the week. Dr. Dahlquist assisted us in class.
References
Dahlquist, K. Master_sheet_dGLN3.
LMU BioDB 2024. (2024). Week 9. Retrieved Mar 20, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_9
LMU BioDB 2024. (2024). Week 9. Retrieved Mar 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
Assignment Pages
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
Individual Journal Entry Pages
- ckaplan Week 1
- ckaplan Week 2
- SIR2 Week 3
- AgeAnnoMO Week 4
- ckaplan Week 5
- ckaplan Week 6
- ckaplan Week 8
- ckaplan Week 9
- ckaplan Week 10
- ckaplan Week 11
- ckaplan Week 12
- ckaplan Week 13
- ckaplan Week 14
- ckaplan Week 15
