Record Details

Reverse engineering and analysis of large genome-scale gene networks

DSpace at IIT Bombay

View Archive Info
 
 
Field Value
 
Title Reverse engineering and analysis of large genome-scale gene networks
 
Creator ALURU, M
ZOLA, J
NETTLETON, D
ALURU, S
 
Subject EXPRESSION DATA
ARABIDOPSIS-THALIANA
PHOTOSYSTEM-I
PROTEIN-INTERACTION
CELLULOSE SYNTHESIS
FUNCTIONAL MODULES
MICROARRAY DATA
SEARCH ENGINE
WEB SEARCH
INFERENCE
 
Description Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. To enable fast and accurate reconstruction of large networks, we developed Tool for Inferring Network of Genes (TINGe), a parallel mutual information (MI)-based program. The novel features of our approach include: (i) B-spline-based formulation for linear-time computation of MI, (ii) a novel algorithm for direct permutation testing and (iii) development of parallel algorithms to reduce run-time and facilitate construction of large networks. We assess the quality of our method by comparison with ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and GeneNet and demonstrate its unique capability by reverse engineering the whole-genome network of Arabidopsis thaliana from 3137 Affymetrix ATH1 GeneChips in just 9 min on a 1024-core cluster. We further report on the development of a new software Gene Network Analyzer (GeNA) for extracting context-specific sub-networks from a given set of seed genes. Using TINGe and GeNA, we performed analysis of 241 Arabidopsis AraCyc 8.0 pathways, and the results are made available through the web.
 
Publisher OXFORD UNIV PRESS
 
Date 2014-10-17T05:47:07Z
2014-10-17T05:47:07Z
2013
 
Type Article
 
Identifier NUCLEIC ACIDS RESEARCH, 41(1)
http://dx.doi.org/10.1093/nar/gks904
http://dspace.library.iitb.ac.in/jspui/handle/100/16104
 
Language en