Question: Chip Databases?
4
gravatar for Dejian
9.8 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

Are there some databases specifically collecting data about ChIP, ChIP-chip, and ChIP-seq?

database chip-seq • 7.8k views
ADD COMMENTlink modified 5.4 years ago by marcomendozabpn0 • written 9.8 years ago by Dejian1.3k
7
gravatar for Pierre Lindenbaum
9.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

try NCBI GEO: http://www.ncbi.nlm.nih.gov/geo/

ADD COMMENTlink written 9.8 years ago by Pierre Lindenbaum131k
3

Balance, Pierre's answer is spot on for your posted question. Please can you amend your question so that it reflects what you actually want to know about? It's too vague at the moment.

ADD REPLYlink written 9.8 years ago by Daniel Swan13k

Thank you, Pierre. But I don't think GEO is a ChIP database although there may be ChIP-chip or ChIP-seq data. I am thinking that ChIP databases can be useful to investigate regulation of gene expression.

ADD REPLYlink written 9.8 years ago by Dejian1.3k
6
4
gravatar for Casey Bergman
9.8 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

For Drosophila and C. elegans, the modENCODE project has scores of ChIP-chip and ChIP-seq datasets.

For Drosophila you can also take a look at data compiled in Flynet.

There are a few mammalian ChIP-chip/ChIP-seq datasets (ids OREGDS00006-OREGDS00014) included in the ORegAnno database . e.g. http://www.oreganno.org/oregano/datasetview.action?dsid=OREGDS00006

EDIT:

A new Chip DB for mammals is now out with data for 492 experiments: http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

Ensembl has just announced the inclusion of 243 chip datasets in their regulatory build: http://www.ensembl.info/blog/2011/04/05/243-encode-chip-seq-experiments/

ADD COMMENTlink modified 13 months ago by RamRS30k • written 9.8 years ago by Casey Bergman18k

Thanks for your update.

ADD REPLYlink written 9.6 years ago by Dejian1.3k
3
gravatar for Ian
9.8 years ago by
Ian5.7k
University of Manchester, UK
Ian5.7k wrote:

Such a thing would be great, but as far as i know there isn't a central database, apart from what you can find in GEO or ArrayExpress.

MPromDb has a lot of data sets http://gdvtk.wistar.upenn.edu/data.html. But they are mammalian.

You can also find a lot of data sets at the UCSC browser, there are an increasing number of ENCODE whole genome studies coming through. This does tend to be genome version specific though, for example there is a lot of data for human hg18, but a lot less for hg19.

ADD COMMENTlink written 9.8 years ago by Ian5.7k
0
gravatar for marcomendozabpn
5.4 years ago by
France
marcomendozabpn0 wrote:

I would like to mention that we have setup a database hosting quality scores for ChIP-seq and enrichment related public datasets.

This database www.ngs-qc.org is currently hosting more than 21,000 public entries and we are working in having basically all GEO entries indexed. Several functionalities were also included and exciting things are in preparation so I advice you to keep an eye o it.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by marcomendozabpn0
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