i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.
Bottom Line: As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data.The underlying processing method is based on a ranking-and-recovery procedure, allowing accurate determination of enrichment across heterogeneous datasets, while also discriminating direct from indirect target regions through a 'leading edge' analysis.Use of i-cisTarget is free and open to all, and there is no login requirement.
Affiliation: Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.Show MeSH
Related in: MedlinePlus
Mentions: As an example we use the ChIP-seq peaks of EWS-FLI1 as input. The authors ChIP'ped the C-terminal portion of FLI1 gene in two Ewing sarcoma cell lines (A673 and SK-N-MC) and defined the 1785 peaks that are present in both cell lines as the ‘core set of EWS-FLI1’ binding sites (provided in the Supplementary Table S1 of the corresponding paper). i-cisTarget analysis on this core set of binding sites identified the motif of the fusion product as the first motif (Figure 2c, i-cisTarget results on the website). Interestingly, ENCODE tracks of PolII ChIP-seq and DNAseI-seq on the Ewing sarcoma cell line SK-N-MC are highly ranked in the results. In addition, the remaining enriched features indicate a vast presence for ETS-family transcription factor motifs and this is indeed in agreement with the authors’ claim that the EWS-FLI1 oncogenic protein displaces ETS-family members from their native binding sites.
Affiliation: Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.