AlleleSeq: analysis of allele-specific expression and binding in a network framework

摘要: To study allele-specific expression (ASE) and binding (ASB), that is, differences between the maternally paternally derived alleles, we have developed a computational pipeline (AlleleSeq). Our initially constructs diploid personal genome sequence (and corresponding personalized gene annotation) using genomic variants (SNPs, indels, structural variants), then identifies events with significant in number of mapped reads maternal paternal alleles. There are many technical challenges construction alignment to address, for example, bias mapping reference allele. We applied AlleleSeq variation data NA12878 from 1000 Genomes Project as well matched, deeply sequenced RNA-Seq ChIP-Seq sets generated this purpose. In addition observing fairly widespread behavior within individual functional (including results consistent X-chromosome inactivation), can interaction ASE ASB. Furthermore, investigate coordination ASB multiple transcription factors regulatory network framework. Correlation analyses motifs show mostly coordinated ASE.