Home Predictions Enhancers TFactors TFactorsGeneSets OtherFlies MatScan IDconverter Downloads Help

CBS: an open platform that integrates predictive methods and
epigenetics information to characterize conserved regulatory
features in multiple Drosophila genomes

Enrique Blanco* and Montserrat Corominas
BMC Genomics 13:688 (2012)

Information about the composition of regulatory regions is of great value for
designing experiments to functionally characterize gene expression. The multiplicity
of available applications to predict transcription factor binding sites in a particular
locus contrasts with the substantial computational expertise that is demanded to manipulate
them, which may constitute a potential barrier for the experimental community. CBS
(http://compfly.bio.ub.es/CBS) is a public platform of evolutionarily conserved binding sites
and enhancers predicted in multiple Drosophila genomes that is furnished with published
chromatin signatures associated to transcriptionally active regions and other experimental
sources of information. The rapid access to this novel body of knowledge through a
user-friendly web interface enables non-expert users to identify the binding sequences
available for any particular gene, transcription factor or genome region. The CBS platform
is therefore a powerful resource that provides tools for data mining individual sequences
and groups of coexpressed genes with epigenomics information to conduct regulatory
screenings in Drosophila.

CBS current stats (v 1.0, September 2012):
  • Information for 13,678 genes (21,984 RefSeq transcripts) of D. melanogaster
  • 27,868,614 phylogenetically conserved sites for 346 distinct TFs
  • 15,454 locus that show modENCODE histone marks of potential enhancers
  • 13,326 locus that show modENCODE histone marks of potential enhancers lacking of TSS
  • 6,269 locus that show modENCODE histone marks of potential active enhancers
  • 4,847 locus that show modENCODE histone marks of potential poised enhancers
  • 897 experimentally validated CRMs imported from REDfly
  • 52,724 predictions imported from the BLS collection
  • Computational predictions for 22,763 orthologous predictions in 10 additional species
    (D.ananassae, D.erecta, D.grimshawi, D.mojavensis, D.persimilis,
    D.pseudoobscura, D.sechellia, D.simulans, D.virilis, D.yakuba
    )






To report problems or provide suggestions, please send an e-mail to eblanco at ub.edu


CBS: an open platform that integrates predictive methods and
epigenetics information to characterize conserved regulatory
features in multiple Drosophila genomes
.
BMC Genomics 13:688 (2012)
Updated in May 31 2013 11:48:57