i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.
Bottom Line: Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight matrices) and experimental data tracks (e.g. from ENCODE, Roadmap Epigenomics) that are enriched in the input set of regions.As experimental data tracks we include transcription factor ChIP-seq data, histone modification ChIP-seq data and open chromatin data.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.