Condition of Use
cisMEP is free for both academic and commercial users.
Reference to cite
If you use cisMEP, please cite:
Tzu-Hsien Yang, Chung-Ching Wang, Po-Cheng Hung and Wei-Sheng Wu.
cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.
BMC Systems Biology 2014, 8 (Suppl 4): S8-10.1186/1752-0509-8-S4-S8.
Construction of cisMEP
cisMEP gathered the computationally identified CRM screening results and collected the literature-curated TFBS location data and nine genres of epigenetic data.

a) We have performed different CRM prediction algorithms and gathered these screened potential CRMs for comparative cross-referencing.
  • First, we generated the sequences used for genome-wide CRM screening by extending the genome-wide TFBSs 3 kb upstream and downstream respectively.
  • Second, we collected the binding motif data in the PFM format from JASPAR and adopted the sequence conservation information across different species from the MAVID multiple alignment results.
  • Thrid, we used the above three datasets to perform the genome-wide CRM screening and collected the potential CRM results. Five tools were suitable and selected for the analysis.
  • Finally, for comparative analysis of the results, we classified the potential CRMs obtained from different CRM prediction tools into nested sets and took the minimal sequences in the nested sets as the representing CRMs.
(CRMs forming a nested set are in the same colour and the minimal representing CRM is circumscribed with a dash frame.)

b) The genomic epigenetic marks are mapped to the locations of these potential CRMs for prediction confidence assessment and potential CRM function determination.
  • Nine kinds of epigentic data were collected.
  • Literature-curated CRMs were further retrieved to distingush putative and known CRMs.