Show simple item record

dc.creatorChandrashekar, P
dc.creatorAhmadinejad, N
dc.creatorWang, J
dc.creatorSekulic, A
dc.creatorEgan, JB
dc.creatorAsmann, YW
dc.creatorKumar, S
dc.creatorMaley, C
dc.creatorLiu, L
dc.date.accessioned2020-12-16T14:53:35Z
dc.date.available2020-12-16T14:53:35Z
dc.date.issued2020-01-01
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/4505
dc.identifier.other32176769 (pubmed)
dc.identifier.urihttp://hdl.handle.net/20.500.12613/4523
dc.description.abstract© The Author(s) 2019. Motivation: Functions of cancer driver genes vary substantially across tissues and organs. Distinguishing passenger genes, oncogenes (OGs) and tumor-suppressor genes (TSGs) for each cancer type is critical for understanding tumor biology and identifying clinically actionable targets. Although many computational tools are available to predict putative cancer driver genes, resources for context-aware classifications of OGs and TSGs are limited. Results: We show that the direction and magnitude of somatic selection of protein-coding mutations are significantly different for passenger genes, OGs and TSGs. Based on these patterns, we develop a new method (genes under selection in tumors) to discover OGs and TSGs in a cancer-type specific manner. Genes under selection in tumors shows a high accuracy (92%) when evaluated via strict cross-validations. Its application to 10 172 tumor exomes found known and novel cancer drivers with high tissue-specificities. In 11 out of 13 OGs shared among multiple cancer types, we found functional domains selectively engaged in different cancers, suggesting differences in disease mechanisms.
dc.format.extent1712-1717
dc.language.isoen
dc.relation.haspartBioinformatics
dc.relation.isreferencedbyOxford University Press (OUP)
dc.rightsCC BY-NC
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectAlgorithms
dc.subjectGenes, Tumor Suppressor
dc.subjectHumans
dc.subjectMutation
dc.subjectNeoplasms
dc.subjectOncogenes
dc.titleSomatic selection distinguishes oncogenes and tumor suppressor genes
dc.typeArticle
dc.type.genreJournal Article
dc.relation.doi10.1093/bioinformatics/btz851
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.creator.orcidKumar, Sudhir|0000-0002-9918-8212
dc.date.updated2020-12-16T14:53:32Z
refterms.dateFOA2020-12-16T14:53:36Z


Files in this item

Thumbnail
Name:
Somatic selection distinguishes ...
Size:
409.3Kb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record

CC BY-NC
Except where otherwise noted, this item's license is described as CC BY-NC