FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer

被引：235

作者：

Fu, Yao ^{[1
]}

Liu, Zhu ^{[2
]}

Lou, Shaoke ^{[3
]}

Bedford, Jason ^{[1
]}

Mu, Xinmeng Jasmine ^{[1
,4
]}

Yip, Kevin Y. ^{[3
]}

Khurana, Ekta ^{[1
,5
,6
]}

Gerstein, Mark ^{[1
,5
,7
]}

机构：

[1] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA

[2] Fudan Univ, Sch Life Sci, Shanghai 200433, Peoples R China

[3] Chinese Univ Hong Kong, Dept Comp Sci & Engn, Shatin, Hong Kong, Peoples R China

[4] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

[5] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

[6] Weill Cornell Med Coll, Dept Physiol & Biophys, New York, NY 10065 USA

[7] Yale Univ, Dept Comp Sci, New Haven, CT 06520 USA

来源：

GENOME BIOLOGY | 2014年 / 15卷 / 10期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

TERT PROMOTER MUTATIONS; SOMATIC MUTATIONS; DIFFERENTIAL EXPRESSION; PERSONAL GENOMES; ENHANCERS; PHOSPHORYLATION; ANNOTATION; ELEMENTS; NETWORK; GENES;

D O I：

10.1186/s13059-014-0480-5

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：15

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