It depends a little bit on where and which TFs you're looking for. But in general I'd suggest the following way:

1. Put your set of sequences into Blast2go (available on-line). This will give you partial annotations (which are the subject of checking anyway), which you can of course use but I'd suggest to go for domain assignments. Don't look at GO terms (they are not that much informative), but concentrate on the InterPro predictions: these are the predictions made by InterProScan tool for protein domains. Your task is basically to extract proteins with DNA-binding domains (because we define the TFs as DNA-binding regulatory proteins).

2. To get the idea which domains you need, go to DBD (already menatoned in one of the previous posts. There you will find (at "Browse families") the full list of DNA binding domains described so far in TFs. I think DBD is a really good collection.

3. Extract the PFAM and Superfamily accessions from DBD.

4. Now your task is to compare 2 lists: the result of the Blast2go (=InterProScan predictions for domains) and DBD domain list (DNA-binding domains). The overlap is you list of potential TFs! Moreover, you will have already the assignments to particular TF families (which are classified based on the DNA-binding domains).

I hope this helps. The sorting can be done in Excel, but for the final extraction (comparison of the lists) you would need a small script.

Good luck!

Try DAVID: http://david.abcc.ncifcrf.gov/

I use DAVID a lot but I guess that they don't have what I am looking for. It only change gene symbols from one form to another. It doesn't really extract the transcription factors from a list of genes.

Try MetaCore from GeneGo http://www.genego.com/

For vertebrates (and maybe animals in general) I'd go for DBD: http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Home

Thanks a lot for answering. I guess the best to work with me is http://www.maayanlab.net/X2K/ it's really interesting and straight forward. In addition there is another interesting tool which is http://tfcones.fugu-sg.org/cgi-bin/genes.pl?sp=human&str=&fam=GTF but I am not really sure about its robustness. The problem with DAVID is that it mixes the transcription factors with other regulatory proteins to put them in one category called (Positive/negative regulation of transcription). One can't elucidate which of which is a transcription factor.

I didn't tell you about TRANSFAC because it costs money to gain access. It might be useful to you, though. Here is a webpage synopsis: http://www.biobase-international.com/product/transcription-factor-binding-sites

Dear Ala,

For the case of human proteins (but even for its parlogs) you can seek at the GeneCard Database (http://www.genecards.org/) which offers a quite complete functional characterization. Best regards.

Daniel

It depends a little bit on where and which TFs you're looking for. But in general I'd suggest the following way:

1. Put your set of sequences into Blast2go (available on-line). This will give you partial annotations (which are the subject of checking anyway), which you can of course use but I'd suggest to go for domain assignments. Don't look at GO terms (they are not that much informative), but concentrate on the InterPro predictions: these are the predictions made by InterProScan tool for protein domains. Your task is basically to extract proteins with DNA-binding domains (because we define the TFs as DNA-binding regulatory proteins).

2. To get the idea which domains you need, go to DBD (already menatoned in one of the previous posts. There you will find (at "Browse families") the full list of DNA binding domains described so far in TFs. I think DBD is a really good collection.

3. Extract the PFAM and Superfamily accessions from DBD.

4. Now your task is to compare 2 lists: the result of the Blast2go (=InterProScan predictions for domains) and DBD domain list (DNA-binding domains). The overlap is you list of potential TFs! Moreover, you will have already the assignments to particular TF families (which are classified based on the DNA-binding domains).

I hope this helps. The sorting can be done in Excel, but for the final extraction (comparison of the lists) you would need a small script.

Good luck!

Have you tried BioCyc.org?

Hi Ala, Excellent resource is http://genome.ucsc.edu/ENCODE/ . Try Data mining with the UCSC Table Browser. It will take you to the UCSC Table browser. There you set group: Regulation, track : Txn Factor ChIP. This will take you to the table of transcription factor binding sites. Remove check-box mark "Send output to Galaxy" , check file type returned to plain text and click get output. In your browser you will get the table, in which the column name contains transcription factor identifiers. You can download this table and match your gene list against the "name" column. I believe you will be able to identify TFs of human, mouse corresponding to the genes in your list. Kind regards.

You can scan Pfam for these genes, and parse for genes which are annotated as transcription factor or transcription factor related. You can also search for your genes in plantTFDB, if these genes are from some plant.

I would recomment you run GO2BLAST annotation, then look for interpro and Pfam domains, hiting for transcription factor or transcription factor like genes

Submissions by Ekaterina Shelest is a good platform to explore ! Thanks

If you are interested in human genes, this review contains a comprehensive list of potential transcription factors:

Vaquerizas et al 2009 "A census of human transcription factors: function, expression and evolution".

Nat Rev Genet 10:252-63 PMID: 19274049

If you are working in an organism other than humans, the approach detailed within might be of some use in comprehensively identifying TFs.

You can simple try ingenuity.com . IPA is a very good tool for analysis of gene expression data and there is a trial version.

If you are specifically interested in a human curated list, see this paper:

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Source

There is a list of transcription factors in supplementary file 3.

Olivier

Regarding the paper that has been frequently recommended above,

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.,

Have they used the same methods to update this list of transcription factors since their 2009 publication? I've had a look but can't find anything.

You can try ProtFun prediction tool to predict function of the protein.

http://www.cbs.dtu.dk/services/ProtFun/

If you have a list of HUGO symbols, you can use the DAVID database functional annotation tool. http://david.abcc.ncifcrf.gov/tools.jsp Upload your list and select functional annotation table and then search for GOTERM_MF_FAT for transcription factor.

Or you can use AMIGO. http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?action=advanced_query&session_id=4850amigo1376398428

Upload a text file with your gene symbols and make sure you search by genes.

go to http://www.plantgrn.org/PlantTFcat/ you will find transcription factor

Use one of the many gene ontology tools. Some are free or use their trial licenses. e.g GENEGO, Ingenuity (IPA), AMIGO, DAVID EASE, GATHER, NEXTBIO They all provide TF annotation from upload of gene symbol.

Try also the GENOMATIX website. It is a very useful bioinformatic tool for that kind of information.

For human, mouse and rat list of genes or proteins,

it is very comfortable to identify TFs in one step with the free account

http://genexplain.com/genexplain-platform-1

Identification is done based on recently published comprechensive classifiaction of transcription factors by Edgar Wingender

http://www.edgar-wingender.de/huTF_classification.html

TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170 (2013). doi: 10.1093/nar/gks1123 (http://nar.oxfordjournals.org/content/41/D1/D165.long)

PlantTFcat : http://plantgrn.noble.org/PlantTFcat/

input sequence size limit: 100M.

Use DAVID as gene ontology tool. Then, use DAVID information to get network between detected genes by Cytoscape software