Nstojan1 Week 10
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Rows: 4727 filter greater than 0.05 Media:Screenshots.pptx Media:Natalija_Stojanovic_File_New.xlsx
Rows: 4727 filter greater than 0.05 Media:Screenshots.pptx Media:Natalija_Stojanovic_File_New.xlsx
- Purpose: The purpose of this assignment is to analyze a DNA microarray dataset that involves clustering and analysis of gene regulation networks using the GRNsight software.
- Procedure:
- Preparing the microarray data file for loading into STEM:
- Insert a new worksheet into Excel workbook, and make it dCIN5_stem
- Select all the data from "dCIN5_ANOVA" worksheet and Paste Special > paste the values into "dCIN5_stem" worksheet.
- The leftmost column should have a column header "Master Index". Rename it to "Spot". Rename Column B ("ID") to "Gene Symbol" and delete the column named "Standard_Name".
- Filter the data on the B-H corrected value to be > 0.05
- Once it has been filtered, select all of the rows (not header row) and delete the row by right clicking and choosing "Delete Row" from the context menu. Undo the filter, this will cluster only the genes with "significant" change in expression and not the noise.
- Delete all of the columns EXCEPT for the Average Log Fold change columns for each timepoint.
- Rename the columns with just the time and unites, for example 15m,30m,etc.
- If you had #DIV/0! errors, to remove them, open Find/Replace dialog. Search #DIV/0!, but don't put anything in the replace field. Click "Replace all" to remove the errors
- Save the work. Use Save As to saver the spreadsheet as Text. Click OK to warnings and close the file.
- Preparing the microarray data file for loading into STEM:
- Now download and extract the STEM software. Click here to go to the STEM web site.
- Click on the download link and download the stem.zip file to your Desktop.
- Now download and extract the STEM software. Click here to go to the STEM web site.
Extract the file by right-clicking on it and selecting "Extract all" from the menu. This will create a folder called stem. You now need to download the Gene Ontology and yeast GO annotations and place them in this folder. Click here to download the file "gene_ontology.obo". Click here to download the file "gene_association.sgd.gz". Inside the folder, double-click on the stem.jar to launch the STEM program.
