Consistent with this difference from to Rxo1-mediated resistance, the distribution of up-regulated genes in different function categories was similar in response to inoculation with Xoc strain RS105 in OsHsp18.0-CI OE plants and wild-type (Additional file 4: Figure S2) but were quite different between 9804-Rxo1 and 9804 (Zhou et al. 2010).
The numbers of DEGs in different function categories in OE and WT under infection with RS105.
The distributions of the DEGs in the different function categories were also similar (r = 0.993, α = 0.05, n = 40).
The numbers of DEGs in different function categories for 738 commonly up-regulated genes (A) and 29 commonly down-regulated genes (B) between WT and OE induced by RS105.
GO analysis of all 738 genes indicated that the distributions of the DEGs in 34 different function categories were similar to the results described in Additional file 5: Figure S3A.
Next, to determine whether genes of different function categories were overrepresented in high-recombination regions or hotspots, we used a χ test to determine whether genes that are assigned to different functional categories were nonrandomly distributed between these regions.
The genes associated with ethanol tolerance in yeast were also found to be linked to a broad range of different functional categories and biological functions including mitochondrial function, protein sorting, aromatic amino acid metabolism, vacuolar, vesicular and peroxisomal transport [ 3].
In the process of identifying regulators which have an influence on a large fraction of the regulatory network we defined a TF as a global regulator if it regulates more than 20 different genes organized on different transcription units (TU's) and if those genes belong to a minimum of four different functional categories, excluding hypothetical functions.
We grouped together insertion/deletion, stopgain/loss, and splicing variants as loss-of-function variants to compare alternative allele frequency spectra across different functional categories.
Combined Fig. 3 c,d) therefore show that proteins in the same hub have quite large direct function-GO distances, but rarely belong to entirely different function-GO categories.
