Question: Transcription factor of a gene (Humans)
1
gravatar for Natasha
17 months ago by
Natasha30
Natasha30 wrote:

Hello Everyone, I am trying to find the transcription factor,of the gene PFKL, which binds to the regulatory region of the DNA. PFKL is the gene present in human liver. Is there database from where this information can be obtained? I have a set of genes.I wish to look up for the information about the transcription factor of each of the target gene.Finally,I would also like to know whether the transcription factor acts as an activator or a repressor regulating the expression of a given target gene. I would be grateful for any advice

rna-seq R gene • 667 views
ADD COMMENTlink modified 17 months ago by Hussain Ather910 • written 17 months ago by Natasha30
1

In general, this question is not generally answerable, as TFs interact and binding and effects are context and tissue specific.

ADD REPLYlink modified 17 months ago • written 17 months ago by Sean Davis25k

Finding activation or repression relationships between transcription factors and target genes in human,

In the pazar link, listed in the answer to the above query ,I performed the following task,

In the target gene search tab in Pazar, when the name of a TF is given as the search input, I was able to find results of its target genes I wish to do this task the other way round,

i.e Given a gene I wish to know the transcription factor controlling the expression level of the input gene.

Or,is there any means of obtaining a list of the transcription factors specific to a tissue(e.g. liver/pancreas) from any of the databases? If there is a list of transcription factors ,I can look up for the target genes(of my interest) .

I would be grateful for any advice you could provide

ADD REPLYlink modified 17 months ago • written 17 months ago by Natasha30

The pazar site has downloadable versions of their data, so you could do the reverse mapping in bulk if you liked.

ADD REPLYlink written 17 months ago by Sean Davis25k

I can do the reverse mapping if all the transcription factors are known.I have a list of only 10 TFs. I am trying to gather the list of TFs specific to human liver and pancreas from uniprot. Could you please explain what do you mean by reverse mapping?

The target genes reported in pazar for a given TF--Is it from experimental observation?

Thanks a lot for your advice

ADD REPLYlink written 17 months ago by Natasha30

Pretty broad query. Do you have any evidence papers citing it as a target of TF? Search for those. Or look into ENSEMBLE regulatory build or eQTL studies or UCSC browsers to see what TF seats on those genes. If you have list of genes and you want to find upstream TF that seats on those genes you can perform motif enrichment analysis via pecan or Homer or iregulon to find upstream TF binding those genes based on consensus binding sites. But for single genes you would have to check for both pubmed for studies in liver and also genome or regulatory build browsers for such information. Good luck.

ADD REPLYlink written 17 months ago by ivivek_ngs4.8k

I am looking for the transcription factor involved in the downstream.i.e. a TF binds to the operator site followed by activation/repression of the RNA polymerase which binds to a promoter,this in turn is responsible for transcribing the coding sequence.The end result of which is the mRNA. To be specific,I am looking for information about the transcription factor which controls gene expression.

Thanks a lot for the advice

ADD REPLYlink modified 17 months ago • written 17 months ago by Natasha30
1
gravatar for Hussain Ather
17 months ago by
Hussain Ather910
National Institutes of Health, Bethesda, MD
Hussain Ather910 wrote:

Check out DBD http://www.transcriptionfactor.org/index.cgi?Home

ADD COMMENTlink written 17 months ago by Hussain Ather910
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