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I have a list of transcription factors and I am interested in finding out which which genes might be transcribed as a result of the formation of transcription factor complexes with that transcription factor.
Any ideas on good databases? I've seen that ENCODE hosts data from CHIPseq experiments, but I'm not sure if I can find conclusions regarding interactions from this site. I'm looking for a database with known or putative transcription/gene interactions.
Thanks in advance.
MSigDB has a collection (C3:TFT) of gene sets corresponding to transcription factor targets.
Harmonizome has functional terms for genes extracted from over a hundred publicly available resources.
iRegulon takes a sequence-based approach to finding transcription factor targets. There's a Cytoscape app that you can use to find the regulators of a given gene list, or the targets of a particular transcription factor.
Transcription factor binding sites are predicted using a collection of position weight matrices (PWMs) from a number of sources, including Jaspar and TRANSFAC.
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections PLoS Comput Biol. 2014 Jul 24;10(7):e1003731. doi: 10.1371/journal.pcbi.1003731. eCollection 2014 Jul.
In general, there is two options to identify targets for transcription factors: experimental (ChIP-seq) and sequence-based predictions.
The are multiple projects that produce binding data of transcription factors and quantify their peaks across the genome. The advantage here is that you know that binding actually occurs, as opposed to motif predictions. But you need the corresponding experiments.
You already mentioned ENCODE, which is probably the biggest producer of such data. NIH's Roadmap Epigenomics is another one, but that focusses less on TFs.
If you have a gene list and would like to know which transcription factor was likely involved, you can do an enrichment test of your gene set in known TF targets. The ChEA (ChIP Enrichment Analysis) database does this.
Another possibility is to look at binding motifs and see whether your gene list is enriched in those. These will, however, be inactive in a given tissue or cell type if the chromatin is packed or the methylation state of the promotor is unfavorable.
Examples for those are the JASPAR and TRANSFAC databases, or the MSigDB motif gene set (as burger mentioned). You can also query those features using the Ensembl genome database (BioMart, REST).
Most likely, an analysis you will want to perform is to calculate the enrichment in your gene list, e.g. that you got from differential expression in two conditions.
The most convenient way is to use the Enrichr platform, which is a web page that accepts a gene list and will compute enrichment in ChEA, JASPAR, TRANSFAC, etc. You can also download their gene sets.
TRUSST is a manually curated database with around 790 TFs and their target genes. TRUSST Website
