Hello again - A bit more specific help about the IDs from one of the scientists who created the track. Jennifer
>> What is the meaning of the TFBS name? For example, >> V$CREBP1_01 >> V$CREBP1_Q2 >> The TFBS names are transfac IDs. They tend to name them after the transcription factor that binds them, or after the name of the binding site if it has one. >> Are they the binding sites that bind to the same transcription factors >> (because the same name "CREBP1")? and what is the meaning of 01 and Q2 >> at the end? Yes, they are both most likely bound by the same factor. This can be double checked by using the tfbsConsFactors table. The different numbers at the end just refer to different sources that they used to make the matrix. For example, _01 might be from one study, and _02 from a different one. The _Q's usually tend to be compendiums from several studies. >> If I want to categorize TFBS by its associated >> transcription factor, can I just consider TFBS (ex. V$xxxx_yy) with >> the same name i.e. same xxxx to be the same type? I suggest using the tfbsConsFactors table, to be safe. Matt ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group > ----- "Jittima Piriyapongsa" <[email protected]> wrote: > > > From: "Jittima Piriyapongsa" <[email protected]> > > To: [email protected] > > Sent: Thursday, September 17, 2009 8:49:29 PM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] TFBS conserved > > > > Hi, > > > > I have a question regarding "TFBS conserved" track in Table browser. > > What is the meaning of the TFBS name? For example, > > V$CREBP1_01 > > V$CREBP1_Q2 > > > > Are they the binding sites that bind to the same transcription > factors > > (because the same name "CREBP1")? and what is the meaning of 01 and > Q2 > > at the end? If I want to categorize TFBS by its associated > > transcription factor, can I just consider TFBS (ex. V$xxxx_yy) with > > the same name i.e. same xxxx to be the same type? > > > > Thank you. > > > > Jittima > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
