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To detect the difference of gene age during different development stages, the age distribution of genes in each stage was compared with the background distribution of all genes.
For each expression set, co-expressed genes were defined as pairs whose Pearson correlation exceeded the 99%-quantile of the background distribution of all correlation coefficients.
The expression cutoff was calculated based on the background distribution of all genes that were not expressed (raw read count equals 0) in the reference cohort (n = 156 genes).
We compare the abundance of proteins in the different PINs to a background distribution of all proteins for which abundance was measured (Additional file 1: Table S3, data obtained from [ 25]).
Comparing this distribution with the background distribution of all tandems of ZF genes, we were able to conclude that the zinc-finger gene repressors were preferentially located on chromosome 19 when compared with the rest of the genome by a ratio of 7 : 2 zinc-finger gene repressors of ERVs.
A sequence of these distributions (see Figure S1), demonstrates that the distribution of the CCP scores associated with those genes, whose CHR motif is found in the [−100,0] and [0,100] windows, differs significantly from the background distribution (of all the genes), with an enhanced number of genes with CCP scores as high as 5 10.
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Therefore we investigated whether any protein domain families were over-represented in the plant-associated proteobacteria with respect to the background distribution of domains in all Proteobacteria for which complete sequences were available.
The difference between the individual coexpression patterns is further indicated by significant Students t-test scores when the C vw dependent distributions are compared to a background distribution of coexpression coefficients of all protein pairs in the considered organism [see Additional file 1].
The enrichments of these four genes for either the luminal or basal state were unusual when compared to the background distribution of these enrichments across all expressed genes, indicating that these genes are strong indicators of the two states.
To verify this presumption we analyzed the distribution of dN/ dS ratios for indel containing genes in comparison to the background distribution of dN/ dS values in all human genes.
SIX8 is part of a cluster with a strong secretion signal and a significantly higher percentage of aliphatic amino acids than the background distribution for all clusters.
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