Introduction

EnrichR (Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44(W1):W90-W97. and Chen, E.Y., Tan, C.M., Kou, Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).) is a GSE (Gene Set Enrichment) method that infers biological knowledge by performing enrichment of input gene sets with curated biologically relevant prior databases that represent biological functions or functional pathways. The singleCellTK offers an easy to use interface to the EnrichR method and only requires the selection of input genes and the databases against which the genes should be tested.

General Worflow

The figure below describes the workflow of using EnrichR through singleCellTK user interface:

Workflow Guide

An overall workflow guide on how to use EnrichR 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.

  1. Select Cell Annotation & Pathway Analysis tab from the top menu.
  2. Select EnrichR option from the drop-down menu.

  1. Select if you want to upload a gene symbol file using the option Upload file or choose the Select Gene(s) option if you want to select genes from the already uploaded data.

  2. If Select Gene(s) option is selected, you can select the genes from the available data here. Alternatively, you can upload a gene file using the options specified in (9) and (10).

  3. Select databases to test the input genes against. Selecting ALL will test against all available databases and may take long time to compute.

  4. Press Run to start computation of enrichment scores.

  5. Once EnrichR computation is complete, results can be saved to local drive by pressing the Download Results button.

  6. Results are displayed in the table for genes that are significant (adjusted p value < 0.05).

  1. If Upload file option is selected in (3), additional options are displayed to upload the gene symbols file. The file path can be selected here.

  2. Once filed is selected in (9), options to select the parameters of the input file are displayed so the input file is correctly parsed.