Enrichment Map David Tutorial
Outline
This quick tutorial will guide you through the generation of an Enrichment Map for an analysis performed using DAVID Functional Annotation Tool,
To run this tutorial:
- You need to have Cytoscape installed : minimally 2.6.3 must be installed but preferable to have the latest version of cytoscape
- The Enrichment Map plugin must be in the Cytoscape-[Version#]/plugins folder
You need to download the test data: DavidTutorial.zip
Description of the tutorial files contained in the DavidTutorial folder:
- 12hr_topgenes.txt : List of top genes expressed in Estrogen dataset at 12hr - Official Gene Symbol.
- 24hr_topgenes.txt : List of top genes expressed in Estrogen dataset at 24hr - Official Gene Symbol.
12hr_David_Output.txt : Estrogen treatment - 12hr DAVID result chart - Screen shot of where to get DAVID output chart
- 24hr_David_Output.txt : Estrogen treatment - 24hr DAVID result chart
- Estrogen_expression_file.txt: Expression File - Estrogen treatment, Official Gene Name as key.
Instructions
Step 1: Generate DAVID output files
GO to DAVID website - http://david.abcc.ncifcrf.gov/
- Select and copy all genes in the tutorial file 12hr_topgenes.txt
In Upload tab of DAVID interface Paste genes in text box marked Step 1: Enter Gene list
Select Official Gene Symbol in Step 2: Select Identifier
Select Gene list in Step 3: Select List Type
Click Submit list
- Select species: Homo Sapiens
Click Functional Annotation Chart - Screen shot of where to get DAVID output chart
- Download file - This is the file you can use in Enrichment Map (Dataset 1 or 2:Enrichment Results)
Note: repeat these steps for the 24hrs time-point and the file 24hr_topgenes.txt
Stpe 2: Generate Enrichment Map with DAVID Output
- Open Cytoscape
- Click on Plugins / Enrichment Maps / Load Enrichment Results
- Make sure the Analysis Type is set to DAVID/BiNGO
- Please select the following files by clicking on the respective (...) button and selecting the file in the Dialog:
NO GMT file is required for DAVID Analysis
Dataset 1 / Expression: Estrogen_expression_file.txt (OPTIONAL)
Dataset 1 / Enrichments: 12hr_David_Output.txt
Click on "Dataset 2
" to expand the panel Dataset 2 / Expression: leave empty
Dataset 2 / Enrichments 1: 24hr_David_Output.txt (OPTIONAL)
P-value cut-off 0.001
Q-value cut-off 0.05
- Check Overlap Coefficient
Overlap coefficient cut-off 0.6
- Build Enrichment Map
- Go to View, and activate Show Graphics Details
NOTE: if you are using two enrichment sets you will see two different colours of edges in the enrichment map. When the set of genes in the two datasets are different (for example, when you are comparing two different species or when you are comparing results from two different platforms the overlaps are computed for each dataset separately as there is a different set of genes that the enrichments were calculated on. In this case, since the enrichments were reduced to only a subset of most differentially expressed at each time point the set of genes the enrichments are calculated on are different and overlap are calculated for each set separately.)