Question: Databases Of Annotated Regulatory Sequences
2
gravatar for Anima Mundi
7.7 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

Hello,

I would like to you to suggest me databases of annotated regulatory sequences, such as transcription factor binding sites, in a given promoter. The tool, possibly, should be based on literature. An example of the desired output could be the sequence of nanog promoter in mouse with the known binding sites and other regulatory elements somehow marked. Databases of sole regulatory elements are also welcome.

ADD COMMENTlink modified 7.6 years ago by Bert Overduin3.6k • written 7.7 years ago by Anima Mundi2.4k
1

See related posts: http://biostar.stackexchange.com/questions/4815/chip-databases & http://biostar.stackexchange.com/questions/7093/what-is-the-best-public-resource-for-protein-dna-interactions

ADD REPLYlink written 7.7 years ago by Casey Bergman18k
5
gravatar for Bert Overduin
7.7 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

In Ensembl we do a so-called "regulatory build" for human and mouse, based on genome-wide ChIP-Seq data, that results in a set of "best guess" regulatory elements. For detailed information please have a look here.

The results of this regulatory build are shown on the "Regulation" view under the Gene tab (example) or can be added as tracks to the "Region in detail" view under the Location tab using the [Configure this page] option.

ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Bert Overduin3.6k

Thanks, what about other species? Are there different solutions?

ADD REPLYlink written 7.7 years ago by Anima Mundi2.4k

I am afraid we only have this for human and mouse.

ADD REPLYlink written 7.7 years ago by Bert Overduin3.6k
3
gravatar for Casey Bergman
7.7 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

There are two main open-access database of regulatory sequence information curated from the literature: ORegAnno and Pazar. These project have lost some momentum with the advent of chip-seq, but there are now efforts to curate chip-seq data from the literature such as hmChip and the Ensembl regulatory build mentioned by Bert.

ADD COMMENTlink written 7.7 years ago by Casey Bergman18k
1
gravatar for Sean Davis
7.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You might take a look at the UCSC Genome Browser with several of the gene regulatory tracks turned on. Take a look here for an example. If you scroll down to the bottom of the page, you will see the tracks that are turned on. The amount of data for human is much larger, but DNAseI hypersensitivity is a very good general marker of open chromatin and regulatory potential of a genomic location in a particular cellular context.

ADD COMMENTlink written 7.7 years ago by Sean Davis25k

The problem with UCSC, in my opinion, is that when you try to download regulatory sequences from several genomes by scripting you have to solve the great variability in the different fields between different species. Is there a way to overcome this?

ADD REPLYlink written 7.7 years ago by Anima Mundi2.4k
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