The GSVA (Gene Set Variation Analysis) (Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics 14, 7 (2013).) is a popular method for GSE (Gene Set Enrichment) and allows the identification of changes in pathway activity in RNA-Seq data. The Cell Annotation & Pathway Analysis tab in the singleCellTK offers the computation and visualization of pre-selected gene sets through GSVA sub-tab. The gene sets can be selected from several databases integrated within the toolkit or can be uploaded/created by the users.
The figure below describes the workflow of using GSVA through singleCellTK user interface:
Before running the GSVA algorithm, the gene sets must be selected or uploaded through the Import Gene Sets sub-tab from the Data tab in the toolkit menu. An overall workflow guide on how to import/upload gene sets and consequently using them with GSVA sub-tab is described below. This workflow guide assumes that the SingleCell Data* has already been uploaded through the Import Single Cell Data sub-tab.**
Select the Data tab from the singleCellTK top menu.
Select the Import Gene Sets from the drop-down menu.
Users can choose the Upload a GMT file option to upload gene sets directly stored in a GMT file or choose Select from a database option to select gene sets from multiple databases integrated within the toolkit or lastly choose the Paste in your gene set option to paste gene identifiers directly into the user-interface to create a gene set.