how to get target gene from BED format

dwb0211 · 10-25-2009, 09:51 AM

Recently I download the BED file from GEO, the authors used ChIP-Seq to find the ERa bing site genome-wide,but just supply the peak, the question is how to find the likely regulated target genes from these peaks?

here is the format:

Code:

track name=ER_E2 description=ER_E2
chr1	557112	558114
chr1	559459	560286
chr1	998864	999397
chr1	999399	999604
chr1	1004343	1005146
chr1	1070346	1071080
chr1	1305474	1306502
chr1	1358287	1358744
chr1	1776987	1777750
chr1	1820476	1821168
chr1	1922754	1923628
chr1	2131962	2132747
chr1	2325805	2326447
chr1	2368996	2369977
....

when I load all these data in UCSC,there is a error happend,and puzzled me.

Could someone give me some clue convert these bing-sites to target genes?

I know some R language but no idea completely.

here is the website：ftp://ftp.ncbi.nih.gov/pub/geo/DATA/...2_peaks.bed.gz

thx!

What_Da_Seq · 10-25-2009, 04:45 PM

cisgenome has a bunch of useful executables (windows exe and LINUX binaries) and I suggest this one
refgene_getnearestgene
http://www.biostat.jhsph.edu/~hji/ci...s/download.htm

dwb0211 · 10-25-2009, 07:54 PM

thank you for your reply very much,

I used cisgenome for some time,
when i used the tool to 'file format convert--> bed to cod',there is no result but just a flash of command line.I think there could be some problem come from the Bed file,which confuse me much.

could somebody shed some light for me? thx very much

What_Da_Seq · 10-25-2009, 08:26 PM

Just ad a "rank#" column to the beginning and label the next columns "chromosome" "start" "end" If you do not have more than 1.05 Mio rows you can doe it easily in Excel.
This is essentially a cod file format. good luck

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10-25-2009, 09:51 AM	#1
dwb0211 Member Location: china Join Date: Nov 2008 Posts: 10	how to get target gene from BED format Recently I download the BED file from GEO, the authors used ChIP-Seq to find the ERa bing site genome-wide,but just supply the peak, the question is how to find the likely regulated target genes from these peaks? here is the format: Code: track name=ER_E2 description=ER_E2 chr1 557112 558114 chr1 559459 560286 chr1 998864 999397 chr1 999399 999604 chr1 1004343 1005146 chr1 1070346 1071080 chr1 1305474 1306502 chr1 1358287 1358744 chr1 1776987 1777750 chr1 1820476 1821168 chr1 1922754 1923628 chr1 2131962 2132747 chr1 2325805 2326447 chr1 2368996 2369977 .... when I load all these data in UCSC,there is a error happend,and puzzled me. Could someone give me some clue convert these bing-sites to target genes? I know some R language but no idea completely. here is the website：ftp://ftp.ncbi.nih.gov/pub/geo/DATA/...2_peaks.bed.gz thx!

10-25-2009, 04:45 PM	#2
What_Da_Seq Member Location: RTP Join Date: Jul 2008 Posts: 28	cisgenome has a bunch of useful executables (windows exe and LINUX binaries) and I suggest this one refgene_getnearestgene http://www.biostat.jhsph.edu/~hji/ci...s/download.htm

10-25-2009, 07:54 PM	#3
dwb0211 Member Location: china Join Date: Nov 2008 Posts: 10	thank you for your reply very much, I used cisgenome for some time, when i used the tool to 'file format convert--> bed to cod',there is no result but just a flash of command line.I think there could be some problem come from the Bed file,which confuse me much. could somebody shed some light for me? thx very much

10-25-2009, 08:26 PM	#4
What_Da_Seq Member Location: RTP Join Date: Jul 2008 Posts: 28	Just ad a "rank#" column to the beginning and label the next columns "chromosome" "start" "end" If you do not have more than 1.05 Mio rows you can doe it easily in Excel. This is essentially a cod file format. good luck