IODNE

An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer

S. Mounika Inavolu, Jamie Renbarger, Milan Radovich, V. Vasudevaraja, G. H. Kinnebrew, S. Zhang, L. Cheng

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Subnetwork analysis can explore complex patterns of entire molecular pathways for the purpose of drug target identification. In this article, the gene expression profiles of a cohort of patients with breast cancer are integrated with protein-protein interaction (PPI) networks using, simultaneously, both edge scoring and node scoring. A novel optimization algorithm, integrated optimization method to identify deregulated subnetwork (IODNE), is developed to search for the optimal dysregulated subnetwork of the merged gene and protein network. IODNE is applied to select subnetworks for Luminal-A breast cancer from The Cancer Genome Atlas (TCGA) data. A large fraction of cancer-related genes and the well-known clinical targets, ER1/PR and HER2, are found by IODNE. This validates the utility of IODNE. When applying IODNE to the triple-negative breast cancer (TNBC) subtype data, we identified subnetworks that contain genes such as ERBB2, HRAS, PGR, CAD, POLE, and SLC2A1.

Original languageEnglish (US)
Pages (from-to)168-176
Number of pages9
JournalCPT: Pharmacometrics and Systems Pharmacology
Volume6
Issue number3
DOIs
StatePublished - Mar 1 2017

Fingerprint

Precision Medicine
Breast Cancer
Medicine
Optimization Methods
Cancer
Genes
Triple Negative Breast Neoplasms
Breast Neoplasms
Gene
Protein Interaction Maps
Scoring
Atlases
Gene Regulatory Networks
Neoplasm Genes
Phenobarbital
Proteins
Transcriptome
Target Identification
Neoplasms
Gene Expression Profile

ASJC Scopus subject areas

  • Cardiology and Cardiovascular Medicine

Cite this

IODNE : An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. / Mounika Inavolu, S.; Renbarger, Jamie; Radovich, Milan; Vasudevaraja, V.; Kinnebrew, G. H.; Zhang, S.; Cheng, L.

In: CPT: Pharmacometrics and Systems Pharmacology, Vol. 6, No. 3, 01.03.2017, p. 168-176.

Research output: Contribution to journalArticle

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