Transcription Factor Binding Sites

Question

[Davy]

Hi All, I'm trying to find the TFBS poisition weight matrices for the TFs snail, slug, twist, and smad 4 in humans

None of these are in JASPAR, and I've had no luck with TRANSFAC either. Anyone have any idea where I might be able to get these matrices. Failing the matrices I could calculate them myself in R if I knew the sequences they bind to. If anyone knows of somewhere I could download a whole bunch on known binding sequences for these factors it would be very easy to calculate the motifs and matrices.

Thanks in advance for any help, Cheers, Davy.

Answer 1

[Obi Griffith]

Did you try PAZAR? It has entries for snail from Drosophila which you could use to build a PWM using their built in tools. Unfortunately they only have a single sequence (from ORegAnno) for the human SNAI1 TF. Also just one sequence for human slug (SNAI2?). TWIST1 seems to have enough sequences for a decent PWM. SMAD4 just has a smattering of sequences from mouse and frog (none for human). ORegAnno has one TFBS for SMAD4 in mouse.

If you don't find the sequences you need in JASPAR, PAZAR, ORegAnno or TRANSFAC then I'm afraid you might have to do it the hard way. Search the literature for studies on those specific TFs, extract reported sequences and build your own PWMs. Then, for good karma, you might consider submitting them to PAZAR or ORegAnno so that others can benefit. Another possibility is to find ChIP-seq datasets for these TFs from some human studies. Keep in mind those results (as with the smaller binding site studies) will be context-dependent. For example, Kennedy et al (2011) report on 2362 TGFB-induced SMAD4 binding sites in an ovarian cancer cell line.

Answer 2

[razor]

Some more databases:

• http://www.ifti.org/ootfd/
• http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
• http://genome.crg.es/datasets/abs2005
• http://rulai.cshl.edu/TRED