Inferring gene networks: dream or nightmare?

Abstract:

:We describe several algorithms with winning performance in the Dialogue for Reverse Engineering Assessments and Methods (DREAM2) Reverse Engineering Competition 2007. After the gold standards for the challenges were released, the performance of the algorithms could be thoroughly evaluated under different parameters or alternative ways of solving systems of equations. For the analysis of Challenge 4, the "In-silico" challenges, we employed methods to explicitly deal with perturbation data and time-series data. We show that original methods used to produce winning submissions could easily be altered to substantially improve performance. For Challenge 5, the genome-scale Escherichia coli network, we evaluated a variety of measures of association. These data are troublesome, and no good solutions could be produced, either by us or by any other teams. Our best results were obtained when analyzing subdatasets instead of considering the dataset as a whole.

journal_name

Ann N Y Acad Sci

authors

Scheinine A,Mentzen WI,Fotia G,Pieroni E,Maggio F,Mancosu G,de la Fuente A

doi

10.1111/j.1749-6632.2008.04100.x

subject

Has Abstract

pub_date

2009-03-01 00:00:00

pages

287-301

eissn

0077-8923

issn

1749-6632

pii

NYAS04100

journal_volume

1158

pub_type

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