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Discerning static and causal interactions in genome-wide reverse engineering problems

Summary: Discerning static and causal interactions in genome-wide reverse
engineering problems
M. Zampieri, N. Soranzo and C. Altafini
SISSA-ISAS, International School for Advanced Studies
via Beirut 2-4, 34014 Trieste, Italy
January 9, 2008
Background In the past years devicing methods for discovering gene regulatory mechanisms at
a genome-wide level has become a fundamental topic in the field of system biology. The aim is
to infer gene-gene interactions in a more sophisticated and reliable way through the continuously
improvement of reverse engineering algorithms exploiting microarray technologies.
Motivation This work is inspired by the several studies suggesting that co-expression is mostly
related to "static" stable binding relationships, like belonging to the same protein complex, rather
than other types of interactions more of a "causal" and transient nature (metabolic pathway or
transcription factor­binding site interaction). Discerning static relationships from causal ones on
the basis of their characteristic regulatory structures and in particular identifing "dense modules"
with protein complex, and "sparse modules" with causal interactions such as those between tran-
scription factor and corresponding binding site, the performances of different network inference
algorithms in artificial and real networks (derived from E.coli and S.cerevisiae) can be tested and


Source: Altafini, Claudio - Functional Analysis Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA)


Collections: Engineering; Mathematics