Question: Determine Transcription Factors For Genes
7
gravatar for Joel
6.6 years ago by
Joel140
Joel140 wrote:

I have a list of about 500 genes and I have to determine transcription factors for each of these genes. Is there a database from where I could get transcription factors for each of these genes.

Thanks.

database transcription • 16k views
ADD COMMENTlink modified 10 months ago by krishna.ibioinfo0 • written 6.6 years ago by Joel140
5

Your question can be interpreted 2 ways. Are you asking (i) can you tell me which genes are a TF in a list of genes? or (ii) can you tell me which TFs bind to the regulatory regions of a list of genes?

ADD REPLYlink written 6.6 years ago by Casey Bergman17k
5

What is the organism for these genes ? Sometimes you have databases that are ogranism specific.

ADD REPLYlink written 6.6 years ago by Fred Fleche4.2k
4

Again, another example (I've seen three in 10 minutes this morning) where more information must be given in order to provide a better/best answer.

ADD REPLYlink written 6.6 years ago by Larry_Parnell16k

On re-reading your question, I see that it can be interpreted 2 ways. Are you asking (i) can you tell me which genes are at TF in a list of genes? or (ii) can you tell me which TFs bind to the regulatory regions of a list of genes?

ADD REPLYlink written 6.6 years ago by Casey Bergman17k

On re-reading your question, I see that it can be interpreted 2 ways. Are you asking (i) can you tell me which genes are a TF in a list of genes? or (ii) can you tell me which TFs bind to the regulatory regions of a list of genes?

ADD REPLYlink written 6.6 years ago by Casey Bergman17k

Your question can be interpreted 2 ways. Are you asking (i) can you tell me which genes are at TF in a list of genes? or (ii) can you tell me which TFs bind to the regulatory regions of a list of genes?

ADD REPLYlink written 6.6 years ago by Casey Bergman17k

the organism for these genes is Homo sapiens

ADD REPLYlink written 6.6 years ago by Joel140

@casey i am asking which TFs bind to the regulatory regions of a list of genes

ADD REPLYlink written 6.6 years ago by Joel140
7
gravatar for Khader Shameer
6.6 years ago by
Manhattan, NY
Khader Shameer17k wrote:

EDITED ON July 19th.

If you would like to find transcription factor binding sites enriched in your list of genes, try this:

DAVID for the enrichment analysis of TFBSs associated with your genes (given TFBS is involved in the control of the transcription of the gene). Once you uploaded your gene list you have an option to perform enrichment calculations using a variety of annotations. DAVID provides a category called "UCSCTFBS" in default setting this option unchecked. Please click and expand the "ProteinInteractions" and click on "UCSC_TFBS" PS. I am not sure about source of this data set, so far I got only this link the source data on DAVID forum. It will be great if someone can tell more about the data source.

This data is sourced from UCSC TFBS conserved track. See the details here and table schema here.

If you would like to know what transcription factors (in other words, transcription factor targets) may initiate transcription of your 500 genes, try this:

I recently used "Investigate Gene Sets" options in MSigDB to find the transcription factor target information of my dataset.

The data is curated from TRANSFAC, you can do a 'Compute Overlap' of your genes with the list of genes in the dataset. Output includes a p-value to indicate statistical significance and a Gene/geneset overlap matrix to visualize the gene categorized into different transcription factor targets.

Transcription Factor Target Data set is available here.

Also refer to related question on transcription factor target here.

ADD COMMENTlink modified 6.4 years ago • written 6.6 years ago by Khader Shameer17k

Hi, I followed your suggestion but I can't expand the "ProteinInteractions" and I didn't find answers on DAVID'S forum .Maybe my question is so naive, I have taken some time on it. Please give me some tips. Thank you!

ADD REPLYlink written 4.0 years ago by liux.bio90
2
gravatar for Larry_Parnell
6.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

DBD is fine. To that I would add the list of TFs that the FANTOM consortium considers as relevant for ENCODE and other projects involving transcription factors. There is also some information there on regulatory interactions, such as transcriptional regulation.

ADD COMMENTlink written 6.6 years ago by Larry_Parnell16k
0
gravatar for Ron
13 months ago by
Ron660
United States
Ron660 wrote:

Another similar post

How To Identify Targets Of A Transcription Factor ?

ADD COMMENTlink written 13 months ago by Ron660
0
gravatar for ZhouK.R.
12 months ago by
ZhouK.R.0
Sun Yat-sen University, China
ZhouK.R.0 wrote:

Similar answers can be found here ( A: Finding transcriptional regulators of a gene )

ADD COMMENTlink written 12 months ago by ZhouK.R.0
0
gravatar for krishna.ibioinfo
10 months ago by
krishna.ibioinfo0 wrote:

Thank you Zhouk.R. for sharing this impeccable resource. It was crucial time for me to find it out !!

ADD COMMENTlink written 10 months ago by krishna.ibioinfo0
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