Question

Annotation of 100kb region

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3.4 years ago

bioinformatics.queries ▴ 70

Hello everyone

I tried to annotate the 100kb region (eg. 2790000-28000000) using ChIPseeker. I have the annotated table attached. . Can anyone help in understanding how was the promoter (<= 1kb) annotated. How did they determine the promoter using gene start and end site ?

Thank you so much

Annotation • 1.5k views

ADD COMMENT • link 3.4 years ago by bioinformatics.queries ▴ 70

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I don't know if I understand your question, you can find more information in here. Basically they said "the annotation column annotates the genomic location of a given peak. Since some annotations overlap, they are assigned based on priority: Promoter (defined by tssRegion parameter) ; 5' UTR ; 3' UTR ; Exon ....

ADD REPLY • link 3.4 years ago by Lila M ★ 1.3k

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Hi Lila

Thank you so much for your response. Here you may see I tried to annotate 100 kb region which is labelled as start and end in the table. After I annotated using CHIPseeker it gave me the genes falling into the region and the gene start site and end site. They annotated these regions as promoter (<=1 kb). My question is what parameter they used to label this region as promoter? How are TSS determined ? Does the gene start and end site corresponds to transcription start site (TSS) and Transcription end site (TES), respectively. I am just trying to find how was this annotation of promoter region done?

Looking forward hearing from you.

ADD REPLY • link 3.4 years ago by bioinformatics.queries ▴ 70

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I don't know if I understand your question. The basic principle for annotation is to identify the nearest TSS (genes). So the coordinates you have are the coordinates for the genes that fall inside the peak (one peak might be annotated to several genes). As said in the manual "AnnotatePeak assigns peaks to genomic annotation in “annotation” column of the output, which includes whether a peak is in the TSS". But if you have more technical question you can always send an email to the developers.

ADD REPLY • link 3.4 years ago by Lila M ★ 1.3k

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Hi Lila

Thank you so much for your response. I have more technical question as to how the tool has been developed to get the promoter region. As per your suggestion i posted the question on Bioconductor to ask the developer about the tool.

ADD REPLY • link 3.4 years ago by bioinformatics.queries ▴ 70

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You've cross posted this on BioC support - please do not do that; it is bad etiquette.

ADD REPLY • link 3.4 years ago by Ram 44k

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Since it was BioC tool related question, so I posted over there. I just wanted to understand how does the tool works in annotation. It was more of technical question. As Lila suggested so I email developers. The developers suggested to post in Bioc related question.

ADD REPLY • link 3.4 years ago by bioinformatics.queries ▴ 70

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You should have then edited your question or added a comment stating this, so everything stays in a logical thread. Otherwise, it looks like the same question was asked on multiple communities to see which can give you the fastest answer.