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Functions of the modules were inferred using GO annotations.
The functions of the subnetwork modules were inferred by Gene ontology (GO) enrichment analysis.
The "transcriptional modules" were inferred based on a large collections of expression data in S. cerevisiae (Ihmels et al. 2002).
First, the set of protein family annotations was processed with LDA, and 400 potential functional modules were inferred, with each corresponding to a set of Pfam and/or CAZy families.
Since the connections between miRNAs and target mRNAs in our predicted modules were inferred based on inverse expression relationships and computational target predictions, it was unknown if those miRNAs could actually regulate their target genes directly.
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Only five modules are inferred, whereas by eye it is clear from Figures 3 and 4 that there are more than five expression patterns in each species, due to subtle (but likely important) temporal differences.
BN analysis was first applied to reactions in each module, so that BN of each module was inferred, namely local scale BN.
Furthermore, RMs as well as inter-module relations were inferred from the biologically significant patterns.
The promoters of eight and six Module 5 genes were inferred to be bound by Cbf1p in the two ChIP-chip analyses (supplementary table S7, Supplementary Material online).
In addition to confirmatory relationships, i.e. that primary and secondary wall gene modules were correlated with cellulose synthesis, cell wall related characteristics for several other modules could be inferred.
Further, we define 'modules' (groups of highly correlated genes) and determine that in some instances, the relative importance of genes within these modules can be inferred from network connectivity.
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components were inferred
modules were compared
modules were loaded
modules were ported
modules were extended
modules were connected
modules were measured
modules were included
modules were designed
modules were introduced
modules were used
modules were based
modules were set
modules were fabricated
modules were tested
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