In the Cytocape menu bar, select View and * Show Graphic details*. General layout of Cytoscape panel: In addition to the main window where the network is displayed, there are 2 panels: the Control Panel on the left side and the Table Panel at the bottom of the window.ģa. Navigate the enrichment map to gain a better understanding of a EnrichmentMap network. Note: layout will be different for each user (there is a random seed in the layout algorithm) but it does not change the results or interpretation (the connections are the same, only the display is different). You are encouraged to give it a try once you finished the lab with your own GSEA results. If you work with your own data, a way to populate automatically the fields is to drag and drop your GSEA folder in the ‘Data Set’ window. Tip: it will be displayed as 1E-04 in the scientific notation. Set FDR q-value cutoff to 0.0001 (= only gene-sets significantly enriched at a value of 0.0001 or less will be displayed on the map). Mesenchymal will be associated with red nodes because it corresponds to the positive phenotype and Immunoreactive will be associated with the blue nodes because it corresponds to the negative phenotype. Phenotypes: In the text boxes place Mesenchymal as the Positive phenotype Immunoreactive as the Negative phenotype. TIP: this field is optional but recommendedĬlasses: MesenchymalvsImmunoreactive_rnaseq_classes.cls Tip: this field is optional. Ranks: MesenchymalvsImmunoreactive_edger_ranks.rnkĮxpressions : MesenchymalvsImmunoreactive_rnaseq_expression.txt. GMT : Human_GOBP_AllPathways_no_GO_iea_December_24_2015_symbol.gmt Name: leave default or a name of your choice like “GSEAmap”Įnrichments Pos: gsea_report_for_na_pos_1453222854028.xlsĮnrichments Ned: gsea_report_for_na_neg_1453222854028.xls Specify the following parameters and upload the specified files:
Cytoscape clustering plus#
In the ‘Create EnrichmentMap’ window, add a dataset of the GSEA type by clicking on the ‘+’ plus sign.Ģb. These 2 tables are uploaded using the EnrichmentMap App which will create a network of mesenchymal and immunoreactive pathways that have a significant score (FDR EnrichmentMapĪ ‘Create EnrichmentMap window is now opened. One table ( neg) contains all pathways with an enrichment score (significant or not) related to enrichment of the immunoreactive category (negative score). One table ( pos) contains all pathways with an enrichment score (significant or not) related to enrichment of the mesenchymal category (positive score).
We use precomputed results of the GSEA analysis to create an enrichment map with the aim to transform the tabular format in a network to better visualize the relationships between the significant gene-sets: They correspond to Ovarian serous cystadenocarcinoma samples. The data used in this exercise is gene expression data obtained from high throughput RNA sequencing.
Cytoscape clustering how to#
Post analysis (add drug target gene-sets to the network)Īs second part of the exercise, you will learn how to expand the network by adding an extra layer of information.Ī last optional exercise guides you toward the creation of automatically generated cluster labels to the network.
The enrichment tool chosen for this exercise is GSEA but an enrichment map can be created from various gene-set tools using the generic format or the more specific g:Profiler, DAVID or BiNGO formats. Network Visualization and Analysis with Cytoscape: create an enrichment map from GSEA resultsīy Veronique Voisin Goal of the exercise:Ĭreate an enrichment map and navigate through the networkĭuring this exercise, you will learn how to create an EnrichmentMap from gene-set enrichment results. This means that you are able to copy, share and modify the work, as long as the result is distributed under the same license. This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License. Pathways and Network Analysis of -Omics Data 2019
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