Learning Oncogenic Pathways from Binary Genomic Instability Data

DOI10.1111/J.1541-0420.2010.01417.XMaRDI QIDQ3008875zbMATH OpenOpenAlexWikidataFDO

Authors

Publication date 22 June 2011

Published in Biometrics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0908.3882, http://europepmc.org/articles/pmc3020238

zbMATH Keywords

lassoconditional dependencegraphical modelregularized logistic regressionloss of heterozygosity

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50) Generalized linear models (logistic models) (62J12) Genetics and epigenetics (92D10)

Abstract: Genomic instability, the propensity of aberrations in chromosomes, plays a critical role in the development of many diseases. High throughput genotyping experiments have been performed to study genomic instability in diseases. The output of such experiments can be summarized as high dimensional binary vectors, where each binary variable records aberration status at one marker locus. It is of keen interest to understand how these aberrations interact with each other. In this paper, we propose a novel method, exttt{LogitNet}, to infer the interactions among aberration events. The method is based on penalized logistic regression with an extension to account for spatial correlation in the genomic instability data. We conduct extensive simulation studies and show that the proposed method performs well in the situations considered. Finally, we illustrate the method using genomic instability data from breast cancer samples.

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Cited in

(6)

• An Additive Graphical Model for Discrete Data
• Empirical comparison study of approximate methods for structure selection in binary graphical models
• Nonparametric Finite Mixture of Gaussian Graphical Models
• A sparse Ising model with covariates
• Robust and efficient semi-supervised learning for Ising model
• Estimating networks with jumps

Describes a project that uses

Uses Software

• MIM
• glmnet

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