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. However, the version is WS190. This paper (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.) has analyzed this data. And the data has not been updated for years.
EDGEdb (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.) exclaimed has collected the TFBS for TFs in C.elegans, but not maintained any more.
UCSC also does not host the ChIP-seq data of C. elegans from modENCODE.
So my question is: is there a compiled text file for TF-target information for C. elegans?
Best!
2 answers
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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harold.smith.tarheel
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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