Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks

Mehrab Ghanat Bari, Choong Yong Ung, Cheng Zhang, Shizhen Zhu, Hu Li

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 108 Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.

Original languageEnglish (US)
Article number6993
JournalScientific Reports
Volume7
Issue number1
DOIs
StatePublished - Dec 1 2017

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Neoplasm Genes
MHC Class II Genes
Genes
Neoplasms
MHC Class I Genes
Oncogenes
Carcinogenesis
Machine Learning
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks. / Ghanat Bari, Mehrab; Ung, Choong Yong; Zhang, Cheng; Zhu, Shizhen; Li, Hu.

In: Scientific Reports, Vol. 7, No. 1, 6993, 01.12.2017.

Research output: Contribution to journalArticle

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