Database for C. elegans TFBS
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Entering edit mode
5.7 years ago
pengchy ▴ 430

Hi,

Is there a database store the TFBS of C. elegans derived from ChIP-Seq or other experimental methods? Currently, I have the following one methods:

Downloaded the ChIP-Seq data of the 27 TFs from modencode [1]. However, the version is WS190. This paper [2] has analyzed this data. And the data has not been updated for years.

EDGEdb exclaimed has collected the TFBS for TFs in C.elegans, but not maintained any more.

UCSC also not host the ChIP-seq data of C. elegans from modENCODE [4]. WormMine neither [5].

So my question is: is there a compiled text file for TF-target information for C. elegans?

Best!

 

[1] http://wiki.modencode.org/project/index.php/File:S23ws190.tgz

[2] Cheng, C., et al. (2011). "Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data." PLoS Comput Biol 7(11): e1002190.

[3] Barrasa, M. I., et al. (2007). "EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression." BMC Genomics 8: 21.

[4] http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=448834309_IpkGripsp5xSrA4bvXTFsm2FzBOG&clade=worm&org=C.+elegans&db=ce10&hgta_group=allTables&hgta_track=pubsBingBlat&hgta_table=0&hgta_regionType=genome&position=chrII%3A14646301-14667800&hgta_outputType=primaryTable&hgta_outFileName=

[5] http://www.wormbase.org/tools/wormmine/templates.do

TFBS database c.elegans ChIP-Seq • 2.7k views
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Entering edit mode
5.7 years ago

The Walhout lab has published a number of studies of C. elegans transcription factor/binding site interactions (e.g., http://www.ncbi.nlm.nih.gov/pubmed/25905672). Those contain the most up-to-date information.

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This is in vitro data from protein binding microarrays, hence only predicts in vivo binding sites to a certain extent...

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Thank you harold. I will look at this paper.

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5.7 years ago
jurgnjn ▴ 70

The modENCODE comparative regulatory analysis paper from 2014 profiled 93 worm factors in vivo using ChIP. Their peak calls can be downloaded from the companion web site.

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thank you jurgnjn. I will have a look at this paper

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