Directed module detection in a large-scale expression compendium

Qiang Fu; Karen Lemmens; Aminael Sanchez-Rodriguez; Inge M Thijs; Pieter Meysman; Hong Sun; Ana Carolina Fierro; Kristof Engelen; Kathleen Marchal

doi:10.1007/978-1-61779-361-5_8

Directed module detection in a large-scale expression compendium

Methods Mol Biol. 2012:804:131-65. doi: 10.1007/978-1-61779-361-5_8.

Authors

Qiang Fu¹, Karen Lemmens, Aminael Sanchez-Rodriguez, Inge M Thijs, Pieter Meysman, Hong Sun, Ana Carolina Fierro, Kristof Engelen, Kathleen Marchal

Affiliation

¹ Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium.

PMID: 22144152
DOI: 10.1007/978-1-61779-361-5_8

Abstract

Public online microarray databases contain tremendous amounts of expression data. Mining these data sources can provide a wealth of information on the underlying transcriptional networks. In this chapter, we illustrate how the web services COLOMBOS and DISTILLER can be used to identify condition-dependent coexpression modules by exploring compendia of public expression data. COLOMBOS is designed for user-specified query-driven analysis, whereas DISTILLER generates a global regulatory network overview. The user is guided through both web services by means of a case study in which condition-dependent coexpression modules comprising a gene of interest (i.e., "directed") are identified.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Mining / methods*
Databases, Genetic*
Gene Regulatory Networks / genetics*
Internet
Protein Array Analysis*
Software*
Systems Biology / methods*