Download the test data:
Description of the tutorial files contained in the GREATTutorial folder:
TestRegions_ForGREAT.bedExample GREAT genomic region input file.
GreatExprotAll.tsvExample of download GREAT output file.
20140919-public-2.0.2-3vD5MB-hg19-all-gene.txtExample downloaded GREAT gene to region association file.
geneToRegionExpressionFile.txtTransformed gene to region association file downloaded from GREAT.
Step 1: Generate GREAT output files¶
- GO to GREAT website
- Select Species Assembly associated with your data. For this tutorial select Human: GRCh37
- In Test regions click on Choose File
- Navigate to files provided and select TestRegions_forGreat.bed
- Click on Submit
- Once the results page has loaded download all the results - in the Global controls heading click on the down arrow next to Global Export
- Select All data as tsv - greatExportAll.tsv will automatically be downloaded to your default Downloads directory. This is the file you can use in Enrichment Map (Dataset 1 or 2:Enrichment Results)
Step 1B (Optional): Generate Gene to region association file¶
Optional - Download the Gene-to-region used by GREAT and modify it to be used in EM as an expression file.
- In the Global controls heading click on the down arrow next to Global Export
- Select view all region-gene associations
- Next to Gene > genomic region association table [The table on the right hand side of the page] click on Download table as text.
- File will automatically downloaded into your default Downloads directory (file name is similar to DATE-public-2.0.2-3vD5MB-hg19-all-gene.txt where DATE is the date of download. Name will also change depending on the version of GREAT and genome selected).
- Open the downloaded file in Excel.
- Add a row to the top of the file.
- In the first column enter “Name”, and in the second column enter “Description”
Step 2: Generate Enrichment Map with GREAT Output¶
- Open Cytoscape
- Click on Apps / Enrichment Maps / Load Enrichment Results
- Make sure the Analysis Type is set to DAVID/BiNGO/GREAT
- Please select the following files by clicking on the respective (…) button and selecting
the file in the Dialog:
- NO GMT file is required for GREAT Analysis
- Dataset 1 / Expression:
- Dataset 1 / Enrichments:
- Tune Parameters
- P-value cut-off 0.001
- Q-value cut-off 0.05
- Jaccard coefficient cut-off 0.25
- Build Enrichment Map
Step 3: Filtering GREAT results¶
- Once the network starts to build a dialog will pop up asking you how you would
like to filter the GREAT results. There are four options:
- Use Hypergeometric test p-values and FDR only –> Hypergeometric
- Use Binomial test p-values and FDR only. –> Binomial
- Use both hypergeometric and binomial test p-values and FDR. Enrichment result must pass threshold for both tests. –> Both
- Enrichment result must pass one of the above tests to be included in the results –> Either
- Select Both
Step 4: Examining Results¶
- Node (inner circle) size corresponds to the number of genes in dataset 1 within the geneset
- Colour of the node (inner circle) corresponds to the significance of the geneset for dataset 1.
- Edge size corresponds to the number of genes that overlap between the two connected genesets.