For this purpose, the candidate gene can be searched on the gene signature collection to retrieve all available differential expression evidences.
Decorin and MIP-1γ were not detectable in the conditioned medium from MB49, whereas both were readily quantified in the conditioned medium from MB49-I, thus confirming the differential expression evidenced by the antibody array experiment (Fig 4B).
In brief, a pathway-level statistic is used to average differential-expression evidence across all genes (e.g., gene-level scores) in a given pathway (gene set C containing n distinct genes).
To address this concern we computed the number of SNPs per kilobase of the union exons for each of the 16,183 genes and assessed differential expression for evidence of directional bias.
There are two major types of effector families: one comprises shorter proteins (100 150 amino acids), with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300 400 amino acids), with lower levels of differential expression and evidence of purifying selection between paralogs.
When both homeologs were expressed, only 15%0.5%5% of the total) showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks) and non-synonymous nucleotide substitution (Kn) provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place.
Altogether, these results confirmed that rsh-dependent differential gene expression evidenced by oligonucleotide microarray analysis could be reproduced by RT-qPCR.
Thus, evidence for exon-specific differential expression required relatively strong evidence for differential expression in at least one exon and a relative absence of evidence for differential expression in at least one other exon.
We performed a Gene Ontology enrichment analysis on genes that showed evidence of lineage-specific differential expression to search for evidence of directional selection using AmiGO through the Saccharomyces Genome Database [ 22].
These differential expression results provided further evidence that miR-433 and miR-127 produced from the miR-433-127 loci were transcribed from two separate promoters in human, rat, and dog.
