This script takes the latest dorothea dataset of Transcription Factor-Target interactions and transposes it into a .gmt file suitable for The Broad/UCSD's GSEA program. GSEA is an alternative to the more commonly used tool VIPER.
Dorothea allows you to infer TF activity from gene expression data by not looking at the gene expression of the TFs itself but the expression of their direct transcriptional targets. This yields a list of the presumed transcription factors responsible for the temporal change of gene expression for each condition.
The file dorothea.R uses the dorothea R library to read in the dataset which is formatted as follows:
| TF | confidence | target | mor | |
|---|---|---|---|---|
| 1 | Ahr | B | Cyp1a1 | 1 |
| 2 | Ahr | B | Cyp1a2 | 1 |
| 3 | Ahr | B | Cyp1b1 | 1 |
| 4 | Ahr | B | Fos | 1 |
| 5 | Ahr | B | Myc | 1 |
| 6 | Ahr | B | Ugt1a7c | 1 |
| 7 | Ahr | B | Ugt1a6a | 1 |
| 8 | Ahr | B | Ugt1a6b | 1 |
| 9 | Ahr | B | Asap1 | 1 |
| 10 | Ahr | B | Erg | 1 |
| 11 | Ahr | B | Vgll4 | 1 |
| 12 | Ar | A | Abce1 | 1 |
| 13 | Ar | A | Acad12 | 1 |
| 14 | Ar | A | Acad10 | 1 |
| 15 | Ar | A | Ahsg | 1 |
| 16 | Ar | A | Akr1b3 | 1 |
| 17 | Ar | A | Akt1 | 1 |
| 18 | Ar | A | Anapc10 | 1 |
| 19 | Ar | A | Ap2m1 | 1 |
| 20 | Ar | A | Appbp2 | 1 |
and the script rearranges it like this:
| TF | Description | Targets | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ahr | 1 | Cyp1a1 | Cyp1a2 | Cyp1b1 | Fos | Myc | Ugt1a7c | Ugt1a6a | Ugt1a6b | Asap1 | Erg | Vgll4 |
| Ar | 2 | Abce1 | Acad12 | Acad10 | Ahsg | Akr1b3 | Akr1b3 | Akt1 | Anapc10 | Ap2m1 | Appbp2 |
The user can easily select the desired confidence level. See dorothea's paper or the comments in the script for what each confidence level signifies.
The supplied gmt files in this repository contains TF-Target interactions with A, B, C, and D grades.
Dorothea only supports mouse and human. The code required for both is in the script, simply comment/uncomment the one you don't need.
Note: The column that is suppose to be a description in the GMT file is currently just dummy numbers. The script may soon be updated so this field is a link to the TFs Reactome entry.