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| This quick tutorial will guide you through the creation of an additional gene-set on the map | This quick tutorial will guide you through the creation of an additional gene-set on an pre-existing Enrichment Map. It can for example help to localize microRNA, transcription factors or drug targets in enriched pathways displayed on the map. The new gene-set that we want to add to the network is called the signature gene-set. |
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| To run this tutorial: | '''To run this tutorial:''' |
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| * You need to download the test data: [[attachment:gProfilerTutorial.zip]] | * You need to download the test data: [[attachment:PostAnalysisTutorial.zip]] '''Description of the tutorial files contained in the !PostAnalysisTutorial folder:''' * CTCF_DIFF.gmt : List of the genes included in the signature gene-set. * Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt: Original gene-set file that has been used to create the original Enrichment Map * ES12_EM_example.cys: the Enrichment Map on which we want to add the signature gene-set |
Enrichment Map Post Analysis Tutorial
Outline
This quick tutorial will guide you through the creation of an additional gene-set on an pre-existing Enrichment Map. It can for example help to localize microRNA, transcription factors or drug targets in enriched pathways displayed on the map. The new gene-set that we want to add to the network is called the signature gene-set.
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 2 (e.g. 2.8.3)
- It does not work with Cytoscape 3
- Install the Enrichment Map 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
You need to download the test data: PostAnalysisTutorial.zip
Description of the tutorial files contained in the PostAnalysisTutorial folder:
- CTCF_DIFF.gmt : List of the genes included in the signature gene-set.
Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt: Original gene-set file that has been used to create the original Enrichment Map
- ES12_EM_example.cys: the Enrichment Map on which we want to add the signature gene-set