i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.
i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their target enhancers starting from a set of co-expressed genes. 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. 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. We illustrate i-cisTarget on various Ewing sarcoma datasets to identify EWS-FLI1 targets starting from ChIP-seq, differential ATAC-seq, differential H3K27ac and differential gene expression data. Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget.
Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.
Hana
H
Imrichová
Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.
Gert
G
Hulselmans
Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.
Zeynep Kalender
ZK
Atak
Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium.
Delphine
D
Potier
Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium stein.aerts@med.kuleuven.be.
Stein
S
Aerts
D000818:Animals; D001665:Binding Sites; D001859:Bone Neoplasms / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004330:Drosophila / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D050436:Regulatory Elements, Transcriptional; D012512:Sarcoma, Ewing / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
D014157:Transcription Factors