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Issues impacting genetic network reverse engineering algorithm validation using small networks

DSpace at IIT Bombay

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Field Value
 
Title Issues impacting genetic network reverse engineering algorithm validation using small networks
 
Creator VINH, NX
CHETTY, M
COPPEL, R
WANGIKAR, PP
 
Subject Bayesian network
Microarray
Normalized mutual information
Gene regulatory network
Statistical test
PROBABILISTIC BOOLEAN NETWORKS
DYNAMIC BAYESIAN NETWORK
REGULATORY NETWORKS
COMPOUND-MODE
S-SYSTEM
INFERENCE
EXPRESSION
BIOLOGY
ARACNE
 
Description Genetic network reverse engineering has been an area of intensive research within the systems biology community during the last decade. With many techniques currently available, the task of validating them and choosing the best one for a certain problem is a complex issue. Current practice has been to validate an approach on in-silico synthetic data sets, and, wherever possible, on real data sets with known ground-truth. In this study, we highlight a major issue that the validation of reverse engineering algorithms on small benchmark networks very often results in networks which are not statistically better than a randomly picked network. Another important issue highlighted is that with short time series, a small variation in the pre-processing procedure might yield large differences in the inferred networks. To demonstrate these issues, we have selected as our case study the IRMA in-vivo synthetic yeast network recently published in Cell. Using Fisher's exact test, we show that many results reported in the literature on reverse-engineering this network are not significantly better than random. The discussion is further extended to some other networks commonly used for validation purposes in the literature. The results presented in this study emphasize that studies carried out using small genetic networks are likely to be trivial, making it imperative that larger real networks be used for validating and benchmarking purposes. If smaller networks are considered, then the results should be interpreted carefully to avoid over confidence. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction. (C) 2012 Elsevier B.V. All rights reserved.
 
Publisher ELSEVIER SCIENCE BV
 
Date 2014-10-14T12:55:51Z
2014-10-14T12:55:51Z
2012
 
Type Article
 
Identifier BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1824(12)1434-1441
http://dx.doi.org/10.1016/j.bbapap.2012.05.017
http://dspace.library.iitb.ac.in/jspui/handle/100/14458
 
Language en