I'm trying to determine a general region for a promoter relative to a TSS.
I've got data of MAC peaks and their locations and I'd like to check whether these MAC peaks appear somewhere on a promoter region. Therefore I need to determine general a rule of thumb for the promoter region relative to the TSS of genes. For example: 2000 bp upstream and 2000 bp upstream.
Could anyone send me in the right direction?
Many thanks,
Stijn
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robbenstijn •
You can use several database for promoter regions. You can start from Ensembl database. Use Ensembl biomart to download this data. I have also try to define region around 5KB up stream and downstream for promoter regions instead of only 2KB. The reason? I remember read a paper which explain the average, minimum, and maximum distance promoter region from the gene. The maximum is around 5KB I think. You can also try to check this database: http://www.pazar.info/
That's great, thanks! Would you happen to have this piece of literature so I can validate my actions? I tried finding it myself but wasn't able to.
I think I got it from pazar. Maybe you can explore pazar database first.
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What kind of data it is ? TFs ? Histone modification ? Looks like you are trying to find the direct targets of a TF. Generally +/- 500bp from TSS is considered as promoter. If you go beyond like 2kb or 5kb, they would be distal regulatory elements, not direct targets.