Arnab Kumar Maity1, Sang Chan Lee2, Bani K Mallick2, Tapasree Roy Sarkar2,3. 1. Early Clinical Development Oncology Statistics, Pfizer Inc., San Diego, CA 92121, USA. 2. Department of Statistics. 3. Department of Biology, Texas A&M University, College Station, TX 77843, USA.
Abstract
MOTIVATION: It is well known that the integration among different data-sources is reliable because of its potential of unveiling new functionalities of the genomic expressions, which might be dormant in a single-source analysis. Moreover, different studies have justified the more powerful analyses of multi-platform data. Toward this, in this study, we consider the circadian genes' omics profile, such as copy number changes and RNA-sequence data along with their survival response. We develop a Bayesian structural equation modeling coupled with linear regressions and log normal accelerated failure-time regression to integrate the information between these two platforms to predict the survival of the subjects. We place conjugate priors on the regression parameters and derive the Gibbs sampler using the conditional distributions of them. RESULTS: Our extensive simulation study shows that the integrative model provides a better fit to the data than its closest competitor. The analyses of glioblastoma cancer data and the breast cancer data from TCGA, the largest genomics and transcriptomics database, support our findings. AVAILABILITY AND IMPLEMENTATION: The developed method is wrapped in R package available at https://github.com/MAITYA02/semmcmc. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: It is well known that the integration among different data-sources is reliable because of its potential of unveiling new functionalities of the genomic expressions, which might be dormant in a single-source analysis. Moreover, different studies have justified the more powerful analyses of multi-platform data. Toward this, in this study, we consider the circadian genes' omics profile, such as copy number changes and RNA-sequence data along with their survival response. We develop a Bayesian structural equation modeling coupled with linear regressions and log normal accelerated failure-time regression to integrate the information between these two platforms to predict the survival of the subjects. We place conjugate priors on the regression parameters and derive the Gibbs sampler using the conditional distributions of them. RESULTS: Our extensive simulation study shows that the integrative model provides a better fit to the data than its closest competitor. The analyses of glioblastoma cancer data and the breast cancer data from TCGA, the largest genomics and transcriptomics database, support our findings. AVAILABILITY AND IMPLEMENTATION: The developed method is wrapped in R package available at https://github.com/MAITYA02/semmcmc. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Vinicius Bonato; Veerabhadran Baladandayuthapani; Bradley M Broom; Erik P Sulman; Kenneth D Aldape; Kim-Anh Do Journal: Bioinformatics Date: 2010-12-08 Impact factor: 6.937
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Authors: Jemila S Hamid; Pingzhao Hu; Nicole M Roslin; Vicki Ling; Celia M T Greenwood; Joseph Beyene Journal: Hum Genomics Proteomics Date: 2009-01-12