How to find transcription factors in a list of genes?

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Ariadne Penalva

I am not sure for what specific organism you are looking them, but here is a good comprehensive list for TFs of rats/mice and humans

http://www.tfcheckpoint.org/index.php/browse

Also I can redirect you to this thread where someone else asked the same question. You could start looking for something here as well? https://www.biostars.org/p/8042/

Puli Chandramouli reddy

As Ariadne asked, you need to mention the organism you are working on.

In general, you can paste the list of the genes in http://www.uniprot.org/uploadlists/ or http://pantherdb.org/ or https://david.ncifcrf.gov/summary.jsp and get the associated GO terms (functional annotations) and save the file (preferably in tab delimited format). Then you can filter the genes associated with the following two GO terms.

GO:0043565 - sequence-specific DNA binding

GO:0003700 - transcription factor activity, sequence-specific DNA binding

Note: You may need to refine further, as this method gives some of the proteins which do not have transcription factor activity and interact with DNA.

Suipwksiow Wjkp

@Ariadne @Puli @Shaojun, these lists are very helpful! Problem solved! Thanks a lot!

Mohd.Murshad Ahmed

https://www.grnpedia.org/trrust/downloadnetwork.php

Samip Sharma

Hi Suipwksiow Wjkp.

I adopted a simple method for soybean. Firstly, sort the list of the genes (in excel) using the column "Product" or another relevant column with the term "transcription factor". You will have the gene list of possible TFs. Copy and paste the list in a new excel sheet. Find the list of TFs of different families (http://planttfdb.cbi.pku.edu.cn/index.php?sp=Gma). Copy and paste each family next to the list of your sorted genes. Select both columns and find the matching genes using https://trumpexcel.com/compare-two-columns/ (Example: Compare Two Columns and Highlight Matching Data). Now you can find the TFs present in your gene list.

All the best.