COMP participants had been recruited prospectively from 8/2005-7/2009 at Boston Children's Hospital (BCH), DFCI and BWH onto protocol 05127 (Supplementary material: Comparison group protocol 05127), approved by the DFCI IRB.
Strengthening this claim we note also that although the two networks contain many of the same proteins, they are somewhat different from one another in terms of global structure (Additional File 9 - Supplementary Results: Comparison of the MetaCore™ and iRefWeb PPI networks).
Performing a moderated t-statistic differential expression analysis on each data set (Additional File 9 - Supplementary results: Comparison of the ovarian cancer data set and the melanoma data set), we found that the melanoma data set contained 96 DE genes (p-value < 0.1) while the ovarian cancer data set had only 13 DE genes.
Finally, we generated a nonredundant reference chameleon transcriptome encompassing 16,536 human orthologous transcripts, which served as a reference for further analyses and comparisons (supplementary table S4, Supplementary Material online).
Evolutionary rate comparisons (supplementary table S2, Supplementary Material online) demonstrated a significantly reduced substitution rate for human lineage when compared with rodents, a process known as "hominid slowdown" or "fast rats," respectively.
Supervised class comparisons (Supplementary information and Supplementary Table S1) were performed to select genes with differential expression in cell lines grouped according to the presence of the retrovirus in a particular cVIS (Van Agthoven et al, 2009b).
A total of 56 clusters yielded significant (P < 0.05) MK tests between one or more ingroup taxa, and another 18 were significant in all ingroup versus outgroup comparisons (supplementary table S1, Supplementary Material online).
For the population from Uganda, we inferred the frequency of E-V1515 subhamongroups (among chromosomes classified as E-M35* × M293) through Y-STR (short tandem repeats) comparisons (supplementary table S4, Supplementary Material online).
We did not find a significant fold change in the expression levels of Orco in any of the pairwise comparisons (supplementary table S10, Supplementary Material online): −0.46 (in log2 scale) for D. sechellia versus D. melanogaster males, −0.76 for D. sechellia versus D. melanogaster females, 0.07 for D. sechellia versus D. simulans males, and −0.17 for D. sechellia versus D. simulans females.
The stepwise model selection showed that the coefficient of promoter mCG density– NmiR interaction terms significantly deviate from zero in both human macaque and human mouse comparisons (supplementary table S3, Supplementary Material online), suggesting the dependence between promoter methylation and miRNA regulations in determining dN/ dS.
