Question: How to overlap transcription factor binding sites with unstranded transcript promoters
0
gravatar for biorepine
4.5 years ago by
biorepine1.4k
Spain
biorepine1.4k wrote:

Dear Biostars,

I have a set of noncoding transcript genomic co-ordinates in BED format but with out strand information. I need to calculate the enrichment of a sox2 and oct4 binding sites at the promoters of these transcripts. With out strand information, How could I do this analysis ? Any ideas ? 

Thanx in advance

 

ADD COMMENTlink modified 4.5 years ago by Devon Ryan89k • written 4.5 years ago by biorepine1.4k
1
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

The only thing you can do is extend both the 5' and 3'-most bound by whatever you's using to define a promoter and look for enrichment in the combined region.

BTW, why don't you have strand information? Are these novel ncRNAs and you found them with a non-stranded RNAseq kit?

ADD COMMENTlink written 4.5 years ago by Devon Ryan89k

This lincrna set came from unstranded published rna-seq data (http://www.ncbi.nlm.nih.gov/pubmed/22403033).

I didn't understand what you are trying to say (are you suggesting to take the transcript end that is highly enriched with a given transcription factor as a promoter ?). 

ADD REPLYlink written 4.5 years ago by biorepine1.4k

No, I'm suggesting that you take both ends if you aren't sure which one is actually the promoter. If you first look for enrichment and then use the end(s) with enrichment to test for enrichment then you're quite likely to bias things. The safest bet is to just assume either end of the transcript could be the beginning.

ADD REPLYlink written 4.5 years ago by Devon Ryan89k

ok i get it. thanx. do you think this is best solution for this problem ? 

ADD REPLYlink written 4.5 years ago by biorepine1.4k
1

The only other solution that I can think of is to align those lincRNAs against another organism where they've been better annotated. Alternatively, perhaps you can find some directional public datasets and determine things that way.

ADD REPLYlink written 4.5 years ago by Devon Ryan89k
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