Question: binding close to gene
0
gravatar for Sheila
5.3 years ago by
Sheila250
Germany
Sheila250 wrote:

Given the Chip-seq data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46992 ), how to find that if the transcription factor considered in the study have binding sites close to a specific gene of interest (COX-1 in this case)? 

Please suggest easy to use tool or web service !!

 

chip-seq • 1.8k views
ADD COMMENTlink modified 5.3 years ago by Ming Tang2.5k • written 5.3 years ago by Sheila250
2
gravatar for Ming Tang
5.3 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

I think the easiest way is to upload the peak file (bed file) to UCSC genome browser, and manually check if there are any peaks near COX-1.  other tools like PAVIS http://manticore.niehs.nih.gov:8080/pavis/

annotateGenomicRanges  http://cru.genomics.iit.it/AnnotateGenomicRegions/index.jsf

homer, bedtools, bedops  and R packages ChIPpeakAnno and ChIPseeker http://www.bioconductor.org/packages/2.14/bioc/html/ChIPseeker.html

can annotate the whole peak file.

ADD COMMENTlink written 5.3 years ago by Ming Tang2.5k
1
gravatar for Devon Ryan
5.3 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

It'd be simplest to just use the ChIPpeakAnno package in Bioconductor. Alternatively, just import everything as GRanges objects and use the nearest() function with a bit of scripting.
 

ADD COMMENTlink written 5.3 years ago by Devon Ryan91k

Thanks. If possible please post R code.

ADD REPLYlink written 5.3 years ago by Sheila250

I'll just refer to their vignette, which has an example that seems to closely match what you want to do. Go ahead and make a new post if you run into any problems with that.

ADD REPLYlink written 5.3 years ago by Devon Ryan91k
1

see this bug, http://ygc.name/2014/01/14/bug-of-r-package-chippeakanno/

ADD REPLYlink written 4.4 years ago by Guangchuang Yu2.2k

Interesting, thanks for pointing that out. I agree that it should take the strand of a peak (when known) into account and calculate distances accordingly. Has there been any movement on fixing this?

ADD REPLYlink written 4.4 years ago by Devon Ryan91k
1

This is also my motivation of developing ChIPseeker, https://github.com/GuangchuangYu/ChIPseeker

ADD REPLYlink written 4.4 years ago by Guangchuang Yu2.2k

It's unfortunate that you had to develop a package to get around this, but thanks for doing so!

ADD REPLYlink written 4.4 years ago by Devon Ryan91k

ChIPseeker contains more features than ChIPpeakAnno. It's definitely better.

ADD REPLYlink written 4.4 years ago by Guangchuang Yu2.2k

The author don't believe this is an issue as she replied in my blog post.

They don't fix this issue, you can refer to the supplemental file of http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145.

 

ADD REPLYlink written 4.4 years ago by Guangchuang Yu2.2k
1
gravatar for Alex Reynolds
5.3 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

BEDOPS offers a tool for this called closest-features, which finds the nearest query element(s) to each of a set of reference elements. (In your use case, TF binding sites would be query elements, and your genes (say, TSSs) are your reference elements.)

It's very simple to use, and very fast, with a low memory profile. R and libraries often have a habit of loading everything into system memory, which can be a problem if you're working with large datasets. 

To get your TFs ready, you can use the bedops set operation tool to filter your transcription factor set for TF binding sites that overlap ChIP-seq peaks or other regions. Take a look at the --element-of operation.

Then you might use closest-features to look for the nearest ChIP-seq-peak-overlapping-TF to each member of your set of, for example, gene transcription start sites (COX-1, etc.).

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Alex Reynolds28k
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