Transfac - Finding Transcription Factor Binding Sites?

Question

[User 6791]

I'm taking an introductory bioinformatics course and the notes are rather sparse, so I've been left mostly to my own devices to figure things out... on that, if anyone has any suggestions for resources for a beginner in this field(which seems positively massive and daunting) they'd be most appreciated.

Anyhow, I have a homework assignment and I need to find "transcription factor binding sites for the heat shock protein in humans" from the TRANSFAC database. I am looking at what I believe to be the protein in the TRANSFAC database(http://www.genome.jp/dbget-bin/www_bget?tffactor:T00992) and don't see where the binding sites are listed.

A transcription factor is a protein that binds to DNA sequences, right? So how exactly would the binding site be represented in the TRANSFAC database resultset? Am I even looking at the right results in the TRANSFAC DB?

Thanks!

[Qdjm]

"Transcription factor (TF) binding site" sometimes means genomic regions bound by a TF, or sometimes the motif model that describes the DNA sequence binding preferences of the TF, or sometimes genomic regions that contain matches to the motif model. Do you have a sense of which of these three definitions is indicated in your assignment?

[User 59]

There's also more than one 'human heat shock protein' surely?

[Fred Fleche]

It seems that the link you are providing is not on Transfac. It is may be why you are not viewing the related binding site.

[User 6791]

qdjm -- I'm not quite sure, the assignment as I said was very vague. And yes, there are multiple human heat shock proteins. I think the point of the assignment is just to get us to use TRANSFAC to find some information; the professor hasn't covered TF binding sites or human heat shock proteins.

Answer 1

[D. Puthier]

Have a look at the courses given by J. Van Helden. Especially this one. Next you can download Transfac academic version from here. Finally, using the RSAT web serveur, you should be able do get the promoter region of your gene of interest to scan it using any PWM.

[pengchy]

Thank you for the information. Is there possible to downloaded the transfac database public version that published at 2005? The link you provided is from 1997. However, the version 1997 has only half of the 2005 version. Like Matrix, 260 in 1997, but 398 in 2005 version. The statistics of 2005 come from http://www.biobase-international.com/gene-regulation.

Answer 2

[Ian]

HSP90AA1 (aka HSP90/HSP89) is not a transcription factor. Is it possible you are required to look for TFBS controlling this gene?

[User 6791]

That would make sense. I will have the professor clarify and update his notes(he is teaching the class from a book-in-progress he's writing...). Thank you!

Answer 3

[Larry_Parnell]

There are at least 44 different genes encoding heat shock proteins in human. Not one of these is used by MAPPER, a transcription factor binding site algorithm which uses TRANSFAC and JASPAR motifs. None have been identified by FANTOM, a consortium looking at all transcription factors in the human genome. However, a few have been identified has binding to DNA oligos by Xie, Z., Hu, S.H., Blackshaw, S., Zhu, H. and Qian, J. (2009) hPDI: a database of experimental human protein-DNA interactions, Bioinformatics. (In press); http://bioinfo.wilmer.jhu.edu/PDI/. They are HSPE1, HSPA1L, HSPB1 and HSPA5.

Thus, I agree with Ian and suggest that you are supposed to look for binding sites regulating expression of oneo r more of the 44+ heat shock genes.