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Modular gene expression in Poplar: a multilayer network approach
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. (Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, University of Agricultural Sciences, Umeå, Sweden)ORCID iD: 0000-0002-1543-7358
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0002-6002-929X
2009 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 181, no 2, 315-322 p.Article in journal (Refereed) Published
Abstract [en]

* 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.

Place, publisher, year, edition, pages
2009. Vol. 181, no 2, 315-322 p.
National Category
Botany
Identifiers
URN: urn:nbn:se:umu:diva-11508DOI: 10.1111/j.1469-8137.2008.02668.xPubMedID: 19121030OAI: oai:DiVA.org:umu-11508DiVA: diva2:151179
Available from: 2009-01-13 Created: 2009-01-13 Last updated: 2017-12-14Bibliographically approved

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Grönlund, AndreasBhalerao, Rishikesh PKarlsson, Jan
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