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Inferring gene networks: dream or nightmare?: Part 1: challenges 1 and 3

Baralla, Angela and Wieslawa, I. Mentzen and De La Fuente, Alberto (2009) Inferring gene networks: dream or nightmare?: Part 1: challenges 1 and 3. Annals of the New York Academy of Sciences, Vol. 1158 , p. 246-256. eISSN 1749-6632. Article.

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DOI: 10.1111/j.1749-6632.2008.04099.x

Abstract

Inferring gene networks is a daunting task. We here describe several algorithms we used in the Dialogue for Reverse Engineering Assessments and Methods (DREAM2) Reverse Engineering Competition 2007: an algorithm based on first-order partial correlation for discovering BCL6 targets in Challenge 1 and an algorithm using nonlinear optimization with winning performance in Challenge 3. After the gold standards for the challenges were released, the performance of alternative variants of the algorithms could be evaluated. The DREAM competition taught us some strong lessons. Amazingly, simpler methods performed in general better than more advanced, theoretically motivated approaches. Also, the challenges strongly showed that inferring gene networks requires controlled experimentation using a well-defined experimental design. Analyzing data obtained through merging many unrelated datasets indeed resulted in weak performances of all algorithms, while algorithms that explicitly took the experimental design into account performed best.

Item Type:Article
ID Code:1854
Status:Published
Refereed:Yes
Uncontrolled Keywords:Gene networks, network inference, system identification
Subjects:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Divisions:001 Università di Sassari > 01 Dipartimenti > Scienze biomediche
002 Altri enti e centri di ricerca del Nord Sardegna > CRS4 Center for Advanced Studies, Research and Development in Sardinia, Pula > Bioinformatica
Publisher:Blackwell / Wiley
eISSN:1749-6632
Copyright Holders:© 2009 New York Academy of Sciences
Deposited On:18 Aug 2009 10:06

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