Update of the ChipSeq Analysis Pipeline ChiPeAn (Version 2.0)

ChiPeAn analyses data from Chipseq experiments. Input is a bed file containing the genomic positions of the peak regions. This version incorporates one major change by replacing the use of the KEGG database by Reactome (see for details). Additionally, the default genome version is now Human 38 (GRCh38).

Several analysis steps are performed:

1. Retrieval of known TFBSs and neighboring genes The TRANSFAC database and the program MATCH@[TM@] are used to search for known transcription factor binding sites (TFBS) for each of the input peaks. Subsequently, Chipean searches for genes in the neighborhood of each peak in the Ensembl database.

2. Enrichment analysis Enrichment anyalysis is performed both for Gene Ontology Terms (GO) but also for metabolic pathways. In this version, for pathways the use of the KEGG database has been replaced by Reactome. Statistics is performed using the R packages topGO (Gene Ontology) and fdrtool (Reactome).

3. Motif comparison and motif enrichment analysis MEME, DREME and Gibbs sampling are used for motif finding, which is adjustable via several user-set parameters. TOMTOM, a motif comparison tool, uses the results of the motif discovery tools to match them against known motifs from TRANSFAC.

Your HUSAR team 02/28/17

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