NDLI: Hierarchical Probabilistic Interaction Modeling for Multiple Gene Expression Replicates

Content Provider	IEEE Xplore Digital Library
Author	Patton, K.L. John, D.J. Norris, J.L. Lewis, D.R. Muday, G.K.
Copyright Year	2004
Abstract	Microarray technology allows for the collection of multiple replicates of gene expression time course data for hundreds of genes at a handful of time points. Developing hypotheses about a gene transcriptional network, based on time course gene expression data is an important and very challenging problem. In many situations there are similarities which suggest a hierarchical structure between the replicates. This paper develops posterior probabilities for network features based on multiple hierarchical replications. Through Bayesian inference, in conjunction with the Metropolis-Hastings algorithm and model averaging, a hierarchical multiple replicate algorithm is applied to seven sets of simulated data and to a set of Arabidopsis thaliana gene expression data. The models of the simulated data suggest high posterior probabilities for pairs of genes which have at least moderate signal partial correlation. For the Arabidopsis model, many of the highest posterior probability edges agree with the literature.
Sponsorship	IEEE Computer Society
Starting Page	336
Ending Page	346
Page Count	11
File Size	1203957
File Format	PDF
ISSN	15455963
Volume Number	11
Issue Number	2
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-01-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Mathematical model Computational modeling Correlation Gene expression Data models Bayes methods Educational institutions model averaging Bayesian modeling hierarchical posterior probability multiple replicates gene expression modeling
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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