TY - JOUR AU - Fu, Yao AU - Liu, Zhu AU - Lou, Shaoke AU - Bedford, Jason AU - Mu, Xinmeng Jasmine AU - Yip, Kevin Y. AU - Khurana, Ekta AU - Gerstein, Mark PY - 2014 DA - 2014/10/02 TI - FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer JO - Genome Biology SP - 480 VL - 15 IS - 10 AB - Identification of noncoding drivers from thousands of somatic alterations in a typical tumor is a difficult and unsolved problem. We report a computational framework, FunSeq2, to annotate and prioritize these mutations. The framework combines an adjustable data context integrating large-scale genomics and cancer resources with a streamlined variant-prioritization pipeline. The pipeline has a weighted scoring system combining: inter- and intra-species conservation; loss- and gain-of-function events for transcription-factor binding; enhancer-gene linkages and network centrality; and per-element recurrence across samples. We further highlight putative drivers with information specific to a particular sample, such as differential expression. FunSeq2 is available from funseq2.gersteinlab.org. SN - 1474-760X UR - https://doi.org/10.1186/s13059-014-0480-5 DO - 10.1186/s13059-014-0480-5 ID - Fu2014 ER -