Q. Chip on ChipのデータをBEDのカスタムトラックにしてるんだけど、ここに含まれる遺伝子をどうやったら楽にゲットできる？

A. Table browserのintersectionの機能を使えばいいよ

というやりとりがUCSCのMLにあったのでメモっておく。
Table browserはEnsemblのBioMartのようなもの。
BioMartがどういうものかはググってね。
自分ではやらないのだが、やっている同僚へのメールついでにここにも残しておく。

Subject: Re: [Genome] Chip on Chip promotor analysis

> Dear supporter,
> We run an experiment of Chip-Chip on Affymetrix promotor Reverse starnd
> chip. I have prepered a BED file as a results of my analysis and
> uploaded it to your genome broweser as a custom track. What I would like
> is to get a list of gene which my hits (enriched areas) are next to
> genes at their 5 prime. Thus it is not a simple intersection between
> tables rather I need to intersect with known gene but the ones that
> exist up to N base-pairs downstream. Is it possible to do it?
> Thanks in advance,


The table browser can be used to make a custom track of the upstream
regions of known genes as follows:

clade: Vertebrate
genome: Human
assembly: Mar.2006
group: Genes and Gene Prediction Tracks
track: Known Genes
table: knownGene
region: genome

output format: custom track

click "get output"

On the next page, click "Upstream by" and enter how many bases upstream
you are interested in.  The default is 200.  Click on "get custom track in
table browser"

This custom track can be intersected with your custom track in the table
browser.  More information on intersections is available here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection

I hope this is helpful to you.  Please don't hesitate to contact us again
if you require more assistance.

カスタムトラックは追加してgenome browser上で表示されている状態だと、Table browserのTrackプルダウンメニューにも表示され、選べるようになる。最初、デフォルトの状態でいじっていてカスタムトラックの選択方法が分からず、数分はまった。