Thus, coordination between gene duplication and alternative splicing provides resources for functional innovation to expand protein diversity during the evolution of multicellularity.
Instead of averaging among transcribed loci, our analysis is a gene-centric approach, comparing the normalized expression level as well as the effective UTR length of the same gene among diverse tissues, to uncover potential coordination between gene expression and polyadenylation.
Third, although gene transcripts have been assessed using coexpression networks (Oldham et al. 2008; Winden et al. 2009), the lack of coordination between gene transcripts and protein expression indicates that similar work could be a fruitful contribution to our understanding of the networks of interacting proteins underlying phenotypes.
It is clear from these two panels that in each network, the HCGs are divided into two distinct groups of genes in which there is a positive coordination between the genes within each HCGs group and a negative coordination between the genes of the different HCGs groups.
In addition to the set of selected genes characterized as informative, we hypothesize that the coordination between different genes and clusters can yield information as to the overall response of the system and whether the system has undergone significant experimental perturbations, thus indicating whether the experimental result has been successful in capturing an underlying perturbation.
To further explore this hypothesis, we have formulated an algorithm which takes the coordination between different genes into account.
This approach takes advantage on the ability to detect positive and negative coordination patterns between gene pairs under multiple biological perturbations by comparing changes in the intensities of expression signals of treatment versus control in several repeated experiments for each biological perturbation.
First, we simulated a response matrix in which there is no coordination between the different genes by randomly swapping the perturbations for each gene separately and recalculating the entire coordination matrix.
This lack of coordination between the two genes of interest suggests that quantitative measurements of α-tubII and pfg377 transcript accumulation during development would not provide stable estimates of sex ratio; other transcripts may be more suited to this purpose.
In addition, data on functional coordination between multi-function genes are not explicitly stored [ 31].
