Modular gene expression in Poplar: a multilayer network approach.
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.
Grönlund
Andreas
A
Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.
Bhalerao
Rishikesh P
RP
Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.
Karlsson
Jan
J
Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.
D000465:Algorithms; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D032107:Populus / Q000235:genetics*; D025941:Protein Interaction Mapping; D015398:Signal Transduction