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Modular gene expression in Poplar: a multilayer network approach
Author(s) -
Grönlund Andreas,
Bhalerao Rishikesh P.,
Karlsson Jan
Publication year - 2009
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/j.1469-8137.2008.02668.x
Subject(s) - modular design , set (abstract data type) , gene , computer science , scale (ratio) , computational biology , gene regulatory network , network topology , expression (computer science) , gene expression , biology
Summary• By applying a multilayer network approach to an extensive set of Poplar microarray data, a genome‐wide coexpression network has been detected and explored. • Multilayer networks were generated from minimum spanning trees (MSTs) using Kruskal's algorithm from random jack‐knife resamplings of half of the full data set. The final network is obtained from the union of all the generated MSTs. • The gene expression correlations display a highly clustered topology, which is more pronounced when introducing links appearing in relatively few of the generated MSTs. The network also reveals a modular architecture, reflecting functional groups with relatively frequent gene‐to‐gene communication. Furthermore, the observed modular structure overlaps with different gene activities in different tissues, and closely related tissues show similar over‐ and/or under‐expression patterns at the modular scale. • It is shown that including links that appear in a few of the generated MSTs increases the information quality of the network. In other words, a link may be ‘weak’ because it reflects rare signaling events rather than merely a signal weakened by noise. The method allows, from comparisons of random ‘null networks’, tuning to maximize the information obtainable.