Question: Transcription Factor Enrichment From Transcriptome
5
gravatar for Dave Bridges
4.9 years ago by
Dave Bridges1.3k
Ann Arbor, MI
Dave Bridges1.3k wrote:

Is there any tools to detect enrichment of transcription factor targets from microarray/RNAseq data. I have heard that Metacore has this functionality, but is there a freely available mapping of transcription factors to targets that could be queried in a way analogous to the way DAVID or GOseq queries GO/KEGG pathway enrichment?

ADD COMMENTlink modified 15 months ago by jin80 • written 4.9 years ago by Dave Bridges1.3k
4
gravatar for Anthony Mathelier
4.9 years ago by
University of Oslo, Oslo, Norway
Anthony Mathelier840 wrote:

What I would do is to look at the overrepresentation of TF binding profile motifs in the promoter sequences of your target genes. I did it several times with success. You could use the oPOSSUM3 webtool for instance by providing a list of genes and it will look for overrepresented TFBSs in their promoter sequences. You just need to be really careful with the background sequences you use.

ADD COMMENTlink written 4.9 years ago by Anthony Mathelier840
2
gravatar for zellerm
4.8 years ago by
zellerm20
zellerm20 wrote:

DAVID (http://david.abcc.ncifcrf.gov/summary.jsp) can actually perform TFBS enrichment. After uploading a gene list, see the Chart for "UCSC TFBS" under "Protein Interactions", which will show you over-represented TFBS within your gene list as compared to your background list (or the entire genome if none is provided).

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by zellerm20

It doesn't seem to have this function now! If anyone knows any alternative, that'd be extremely useful!

ADD REPLYlink written 2.8 years ago by antonibltrn0

It doesn't seem to have this function now! If anyone knows any alternative, that'd be extremely useful!

ADD REPLYlink written 2.8 years ago by antonibltrn0
0
gravatar for Wrf
4.9 years ago by
Wrf210
Wrf210 wrote:

I thought they did a similar thing in the ENCODE project for humans. Maybe check that out: http://www.ncbi.nlm.nih.gov/pubmed/22955984/

ADD COMMENTlink written 4.9 years ago by Wrf210
0
gravatar for jin
15 months ago by
jin80
jin80 wrote:

For plants, you can try PlantRegMap to find the enriched transcription factors in a set of genes.

ADD COMMENTlink written 15 months ago by jin80
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