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Genome Medicine

, 6:64

5. Systems medicine and informatics

Abstract

We present the `dnet’ package and apply it to the `TCGA’ mutation and clinical data of >3,000 patients. We uncover the existence of an underlying gene network that at least partially controls cancer `survivalness’, with mutations that are significantly correlated with patient survival, yet independent of tumour origin and type. The survivalness network has natural community structure corresponding to tumour hallmarks, and contains genes that are potentially druggable in the clinic. This network has evolutionary roots in Deuterostomia identifying PTK2 and VAV1 as under-valued relative to more studied genes from that era. The `dnet’ R package is available at http:-cran.r-project.org-package=dnet.

AbbreviationsBLCABladder urothelial carcinoma

BRCABreast adenocarcinoma

COADREADColon and rectal carcinoma

FDRFalse discovery rate

GBMGlioblastoma multiforme

GSEAGene set enrichment analysis

HNSCHead and neck squamous cell carcinoma

HRHazard ratio

KIRCKidney renal clear cell carcinoma

KSKolmogorov-Smirnov

LAMLAcute myeloid leukaemia

LRTLikelihood ratio tests

LUADLung adenocarcinoma

LUSCLung squamous cell carcinoma

OVOvarian serous carcinoma

sTOLSpecies tree of life

UCECUterine corpus endometrial carcinoma

Electronic supplementary materialThe online version of this article doi:10.1186-s13073-014-0064-8 contains supplementary material, which is available to authorized users.

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Author: Hai Fang - Julian Gough

Source: https://link.springer.com/







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