Peaks And Nearby Genes

Question

[Dataminer]

Hi!

Consider if you have a peak file from (as an example from MACS tool) and you are interested in knowing which are the refseq genes present near each peak.

how it can be done?

Thank you in advance.

Answer 1

[Martin Morgan]

In Bioconductor, the ChIPpeakAnno package is one way; the biomaRt, rtracklayer, org*, GenomicFeatures, and GenomicRanges packages provide flexibility for more advanced annotation.

Answer 2

[Brad Chapman]

The Cistrome analysis pipeline, a Galaxy instance with ChIP-seq specific functionality from Tao Liu, the author of MACS, has tools to do this:

http://cistrome.org/

Specifically the peak2gene tool under 'Annotate and Visualize':

Input a peak file, and It will search each peak on UCSC GeneTable to get the refGenes near the peak summit/center.

If you want to run it yourself, the implementation is available. The Galaxy XML file is:

https://bitbucket.org/cistrome/cistrome-harvard/src/tip/tools/ceas/peak2gene.xml

and the script is:

https://bitbucket.org/cistrome/cistrome-applications-harvard/src/tip/cistrome-extra-apps/Scripts/PCGA.py

[Dataminer]

peaks2gene is giving me error. This is what my peak file looks like

chr1    559488  559982
chr1    901276  901835
chr1    1041056 1042026
chr1    1126104 1126603
chr1    1137952 1139449
chr1    1436632 1437594
chr1    1499359 1500427
chr1    1540179 1541367
chr1    2148581 2149255
chr1    2312477 2313343
chr1    2447200 2448043
chr1    2563979 2564842
chr1    3361047 3361747
chr1    3763302 3764563
chr1    5974294 5975631
chr1    6181817 6182492
chr1    6375481 6376543
chr1    6536633 6537483
chr1    6607576 6608455
chr1    6684059 6684813
chr1    7943949 7944803
chr1    8406479 8406982
chr1    8685520 868638

It just fails I don't know why...

[Dataminer]

peak2gene implementation @cistrone is failing to give me result. I don't know why but after loading my peak file as soon as I execute the program it fails.

Answer 3

[2184687-1231-83-]

This tool does the gene enrichment analysis, which is one step further:
http://great.stanford.edu/

[Dataminer]

Problem solved. :)

[Dataminer]

I guess this is the one I am looking for..... Will accept your answer after a positive test run of GREAT.... Thank you

[Dataminer]

Hey! I have a small problem with the output section of GREAT, may be I am missing a step can you help me?

My input file looks like this

Chr chrm_start Chrm_End

and when give this file as an input to GREAT, the result section

The result section of genomic region->gene association some how misses the regions and only shows me genes and distance from TSS . Can you tell me what I am missing ....

Answer 4

[Madelaine Gogol]

bedtools closestBed can do this.

Answer 5

[Praneet Chaturvedi]

HOMER : http://homer.ucsd.edu/homer/ngs/annotation.html Inputs : peak file and genome build