Tutorial 1.3 - Run Enrichment Analysis
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Transcript of Tutorial 1.3 - Run Enrichment Analysis
![Page 1: Tutorial 1.3 - Run Enrichment Analysis](https://reader034.fdocuments.in/reader034/viewer/2022051514/54947e13ac7959ff2d8b4bda/html5/thumbnails/1.jpg)
Tutorial 1.3: Run Enrichment Analysis Run an enrichment analysis to test which KEGG pathways are enriched among genes significantly up-regulated in different types of cancer
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Click Enrichment Analysis Button or
select New>Analysis>Enrichment analysis...
STEP 1
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Click Next
STEP 2You have the option of fill automatically any analysis wizard in Gitools with an example to learn to perform the analysis
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Select the format of the data matrix that you will load. In this case is a
Continuous data matrix. And select the file that
contains the data matrix.
STEP 3
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Transform the continous data matrix to a binary matrix by choosing a
transformation criteria. In this case, since the data matrix contains p-values, we want that values lower
than 0.05 are converted to 1 (significantly up-regulated)
STEP 4
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Select the format of the modules file that you will load. In this case is a two columns mappings. And
select the file that contains the data matrix
and click Next
STEP 5
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Select the type of enrichment analysis that you want to run. In this
case we will run a binomial test. Click Next
STEP 6
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Give a name to the analysis and indicate a Folder where to place it.
Click Next.
STEP 7
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Optionally type a Title and Notes for the
analysis that you are running. Click Finish
STEP 8
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Once the calculations are completed you will have a new tab with the details of the analysis.
Click the Results heatmap button
STEP 8
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This heatmap contains the results of your enrichment analysis
Every column corresponds to a column in the data matrix. In this case each column is a tumor type
Every row corresponds to a module. In this case a KEGG pathway
Every cell is the result of one enrichment analysis. The color of each cell indicates if the genes annotated with the KEGG term are enriched among gene up-regulated in this cancer type.