In this example, two data files stored in the server are used. One (the case) is “logged-colorectal-exhausted-allData.csv” which is the scRNA-seq data from exhausted CD8 T cells isolated from human colorectal cancers (“all” means the data are from multiple patients). The other (the control) is “logged-colorectal-exhausted-controlData.csv” which is the scRNA-seq data from non-exhausted CD8 T cells isolated from the nearby colorectal tissue. Since the data are log2-transformed, the “log2-transformed” button under the “What is the data format” is clicked.
Data uploading may take a while, from seconds to minutes, depending on the two files’ size. After uploading the two files, a TF list should be chosen. Instead of using the default human TF list reported by Bahrami et al 2015, the TF list used in the SCENIC package is chosen here.
After data uploading, the user can use the data summary function at the bottom of the “Main Menu” web page to view data. Genes can be ordered on nine attributes. By pressing the down-triangle button at “valueInCase”, genes are ordered on their expression values.
By pressing the down-triangle button at “foldChange”, genes are ordered on their fold changes. The result shows that CXCL13, HAVCR2, CCL3, and PDCD1 are genes with the largest fold changes.
By pressing the down-triangle button at “TF”, the user can identify all TFs.