|
Size: 4859
Comment:
|
Size: 5420
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 11: | Line 11: |
| * 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 (can be installed directly through Cytoscape plugin manager) * The BiNGO plugin must be in the Cytoscape-[Version#]/plugins folder (can be installed directly through Cytoscape plugin manager) |
* You need to have Cytoscape installed : minimally 2.6.3 must be installed but preferable to have the latest version of Cytoscape (e.g. version 3.1) * Install the Enrichment Map and BiNGO plugin from the Cytoscape plugin manager. If you install it manually (e.g. if you need to install a new version that doesn't happen to be in the plugin manager yet), then it must be in the Cytoscape-[Version#]/plugins folder --> '''For Cytoscape 2.8''' * Install the Enrichment Map and BiNGO App from the Cytoscape App manager in cytoscape 3. --> '''For Cytoscape 3.''' |
| Line 33: | Line 33: |
| 1. Change ''Select organism/annotation'' to '''Homo Sapiens''' | 1. Change ''Select organism/annotation'' to '''Homo sapiens''' |
| Line 39: | Line 39: |
| <<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>> | |
| Line 46: | Line 46: |
| * '''NO GMT file is required for DAVID Analysis''' | * '''NO GMT file is required for BiNGO Analysis''' |
| Line 49: | Line 49: |
| * Click on "''Dataset 2 {{attachment:arrow_collapsed.gif}}''" to expand the panel | * Click on "''Dataset 2 {{attachment:Software/EnrichmentMap/DavidTutorial/arrow_collapsed.gif}}''" to expand the panel |
| Line 53: | Line 53: |
| * P-value cut-off `0.01` | * P-value cut-off `0.001` |
| Line 59: | Line 59: |
| <<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>> | * Note: BiNGO accepts both Entrez Gene IDs [e.g.6672] or gene symbols [STAT1] as input. If Entrez Gene IDs have been used as input, the first column of the expression file should contain Entrez Gene IDs. Similarly, if gene symbols have been used as input, the fist column of the expression file should contain gene symbols. <<BR>><<BR>><<BR>> |
| Line 65: | Line 66: |
| 1. Colour of the node (inner circle) and border(outer circle) corresponds to the significance of the geneset for dataset 1 and dataset 2, respectively. | 1. Colour of the node (inner circle) and border(outer circle) corresponds to the significance based on the BiNGO p-value of the geneset for dataset 1 and dataset 2, respectively. |
Enrichment Map BiNGO Tutorial
Contents
Outline
This quick tutorial will guide you through the generation of an Enrichment Map for an analysis performed using the Cytoscape Plugin BiNGO A Biological Network Gene Ontology 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 (e.g. version 3.1)
Install the Enrichment Map and BiNGO plugin from the Cytoscape plugin manager. If you install it manually (e.g. if you need to install a new version that doesn't happen to be in the plugin manager yet), then it must be in the Cytoscape-[Version#]/plugins folder --> For Cytoscape 2.8
Install the Enrichment Map and BiNGO App from the Cytoscape App manager in cytoscape 3. --> For Cytoscape 3.
You need to download the test data: BingoTutorial.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_Bingo_Output.bgo : Estrogen treatment - 12hr BiNGO result chart
- 24hr_Bingo_Output.bgo : Estrogen treatment - 24hr BiNGO result chart
- Estrogen_expression_file.txt: Expression File - Estrogen treatment, Official Gene Name as key.
Instructions
Step 1: Generate BiNGO output files
- Open Cytoscape
- Click on Plugins / Start Bingo v###
Enter the name "12hr_topgenes" in the text box marked Cluster name
Select the box Paste Genes from Text
- Select and copy all genes in the tutorial file 12hr_topgenes.txt. Paste in large text box.
Change Select ontolgy file to GO_full
Change Select organism/annotation to Homo sapiens
Select the box Check box for saving Data
Click on Save BiNGO Data file in:. Navigate to desired folder and Click Save
Click on Start BiNGO
Note: repeat these steps for the 24hrs time-point and the file 24hr_topgenes.txt
Stpe 2: Generate Enrichment Map with BiNGO 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 BiNGO Analysis
Dataset 1 / Expression: Estrogen_expression_file.txt (OPTIONAL)
Dataset 1 / Enrichments: 12hr_Bingo_Output.bgo
Click on "Dataset 2
" to expand the panel Dataset 2 / Expression: leave empty
Dataset 2 / Enrichments 1: 24hr_Bingo_Output.bgo (OPTIONAL)
- Tune Parameters
P-value cut-off 0.001
Q-value cut-off 0.05
- Check Jaccard Coefficient
Overlap coefficient cut-off 0.25
- Build Enrichment Map
- Go to View, and activate Show Graphics Details
- Note: BiNGO accepts both Entrez Gene IDs [e.g.6672] or gene symbols [STAT1] as input. If Entrez Gene IDs have been used as input, the first column of the expression file should contain Entrez Gene IDs. Similarly, if gene symbols have been used as input, the fist column of the expression file should contain gene symbols.
Step 3: Examining Results
Legend:
- Node (inner circle) size corresponds to the number of genes in dataset 1 within the geneset
- Node border (outer circle) size corresponds to the number of genes in dataset 2 within the geneset
- Colour of the node (inner circle) and border(outer circle) corresponds to the significance based on the BiNGO p-value of the geneset for dataset 1 and dataset 2, respectively.
- Edge size corresponds to the number of genes that overlap between the two connected genesets. Green edges correspond to both datasets when it is the only colour edge. When there are two different edge colours, green corresponds to dataset 1 and blue corresponds to dataset 2.
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.