As expected, genes that were expressed at low levels were more variable among cell lines, as shown in the mean versus standard deviation plot (Figure 1B).
As expected, genes containing TEs were on the whole expressed at lower levels than were genes without TEs (Supplementary Fig. 18, KS test, P < 10−13).
Many expected genes to be proteins.
Cutting at the 99 percentile results in 943 genes (expecting 153 by chance), cutting at the 98, 97, 96 and 95 percentiles would result in 1352, 1587, 1792 and 1972 selected genes (305, 458, 611 and 764 randomly expected genes).
At l exon = 3 (3.5 kb), we find that the local maximum for gene expression occurs at m cg = 0.90 (78.1 %) and at l exon = 4 (6kb) there is no longer a local maximum for m cg, and the highest expected gene expression occurs at m cg approaching 100%% (largest gene size in Fig. 6c).
The expected gene diversity (HE) was compared with the expected gene diversity at mutation-drift equilibrium (HEQ) and calculated from the observed number of alleles under an intermediate two-phase model (TPM) assuming 30%% infinite allele model (IAM) and 70%% stepwise mutation model (SMM) (Di Rienzo et al. 1994).
The experimentally-determined gene number at each step was compared with the expected gene number obtained by simulation.
Since these TFs are co-expressed with the aging-related genes it was expected that these genes, at least in part, would be regulated by the co-expressed TFs.
The number of genes correlated with active period deep sleep did not exceed chance (∼404 genes expected at α = 0.05, 431 genes found; FDR = .94- data not shown).
The category 'All' indicates annotations for the entire IAF-45-CD chromosome; 'Unique' indicates annotations for genes unique to IAF-45-CD; 'Expected' indicates the number of unique genes expected if sampled at random from the pool of all unique genes found in the five genomes.
