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We also compared the gene expression relationship of the identified differentially expressed genes in these four cases.
Two lists of coexpressed genes will be shown in a new view for each high-correlated nonlinear expression relationship of the gene of interest.
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Second, if two genes maintain an expression relationship with a certain type of curve, the genes coexpressed with these two genes maintain expression relationships of the same type between them.
This is consistent with the co-expression relationship of the cell cycle and ECM 5 gene sets.
For one particular gene, an EC score is derived by calculating the PCC between the adjacent edge-weights, i.e. the co-expression relationship, of the two networks thus capturing similarity of gene neighbourhoods (Fig. 2).
To determine the expression relationship of REL2 with the leaf shape regulation associated genes, a total of eighteen genes were selected to be analyzed by qRT-PCR (Fig. 9).
And the detailed co-expression relationships of the top 12 related UniGenes listed in Additional File 8.
The co-expression relationships of the genes exhibited correlation coefficients > 0.525 with the query genes, the co-expression graph was depicted by the Pajek program (http://vlado.fmf.uni-lj.si/pub/networks/pajek/).si/pub/networks/pajek/
To understand the co-expression relationships of the genes within M12, we created a network diagram based on the top 200 connections (based on co-expression) between pairs of genes (Fig. 5A).
Several studies also defined miRNA modules by harnessing predicted miRNA target sites in 3′ UTRs and the co-expression relationship of target mRNAs of the same miRNAs (Bryan et al., 2013; Jayaswal et al., 2011; Zhang et al., 2011).
Importantly, it should be noted that the two SND/VND genes misexpressed in 35S::PCN-miRNAd are orthologous to SND2 and NAC7/VND4, not the better characterized SND1 and VND6&7 [8], and the expression relationships of MYBs to putative targets is altered.
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