I have a set of genes and I want to know which transcription factors are overrepresented in these genes.
I know tools like MEME, but I have to provide the sequence rather than just gene names to the program. Any suggestions?
Try this one, it's called ChEA http://amp.pharm.mssm.edu/lib/chea.jsp. I'm not sure if it's currently working.
I would suggest oPOSSUM: http://opossum.cisreg.ca/oPOSSUM3/ . It uses gene IDs rather than DNA sequences. From my experience it helps to test/benchmark the enrichment tool by feeding it a published high quality ChIP-seq data with a single target and then seeing if the enrichment tool returns the right enriched transcription factor.
Hi,
you did not tell us about the organism you are working with. There are TF repositories that use gene identifier or accession number for many TF genes from various model species to download - e.g. at flybase for Drosophila, or DATF for Arabidopsis.
For non-model organism, there are derived databases that infer homology/orthology for protein sequences based onsequence similarity/identity from model organism data.
In case your institution has acces to TransFac, this database collects all sorts of TF related data.
For smaller datasets, you can do it also by hand in reasonable time, if necessary.
There are also TF prediction programs availabe, that predict whether a primary sequence might be from a putative DNA binding protein.
For statistics, enrichment/depletion you should use simple hypergeometric distribution - its easy to use, e.g. in Excel, and it is a robust measure as long as your sample and population is of a considerable size - which is usually the case as all genes of your organism can be used as pupolation and your initial sample gene list is contains 20 or more accessions.
Hi, you can use Enricher (http://amp.pharm.mssm.edu/Enrichr/) which was developed by the same group of ChEA. you can also use InnateDB (http://www.innatedb.com/batchSearchInit.jsp?type=tfbs), GeneCoDis (http://genecodis.cnb.csic.es/) and ToppGene (http://toppgene.cchmc.org/enrichment.jsp). Also you can follow this entry in Biostar (http://www.biostars.org/p/2942/).
Cheers
Hi, again you may also wanna look at the tool Expression2Kinases were the input list of genes is mapped to the associated transcription factors and then the transcription factors represented are related to kinases. This analysis gives you an insight of upstream elements that might govern the expression changes observed in the input genes. See case of studies at http://www.maayanlab.net/X2K/case_studies.html.
Cheers
You might be interested to try this software:
http://www.genexplain.com/site-analysis
It contains dedicated methods to search for TFBS over-represented in the promoters of genes in focus versus promoters of the background set.
Your input could be a table or list of genes with any common identifiers, e.g. Ensembl, Entrez, UniProt, HGNC
How about "Motif Enrichment Tool" just published in NAR.
http://veda.cs.uiuc.edu/cgi-bin/MET/interface.pl
We have recently a new software pipeline called Haystack find TF enriched :
https://github.com/lucapinello/Haystack/blob/master/README.md
It also integrate gene expression data and epigenetic data if you have.
We validated the pipeline in this PNAS paper:
http://www.pnas.org/content/111/3/E344.abstract
Any feedback is well appreciated!
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