Six miRNAs met all the criteria, i.e., Bonferroni P-value<0.05, FDR (Q-value)<0.01, and top fold changes in both sample sets are indicated by the deep shaded rows.
We analyzed the top fold-change I/U-DEGs, 100 Upr and 100 Dnr that were significant (adjusted p-value < 0.05), in order to compare nearly equal numbers of I/U-DEGs, since I/U-DEGs with >2 fold-change were so few.
Second, a study [ 14] comparing early gastric cancer (EGC) with advanced gastric cancer (AGC) - roughly separating stages I and II - also identified a similar differentially expressed gene list of which again COL11A1 (probe 37892_at) was at the top (log fold change: 4.26) followed by COL10A1 and FAP.
Since a t-test was used for microarray data sets on top of a fold change cutoff to define differentially expressed genes, fewer genes with lower expression levels and therefore higher variability will pass the t-test cutoffs.
This subset (Additional file 2) was selected in subsequent steps: first, among the 86 probe sets identified during the microarray analysis (Additional file 1) we selected the top 36 with fold change ≥ |2.5| and p ≤ 0.005.
Third, a study of pancreatic ductal adenocarcinoma [ 15] identified a list of genes overexpressed in whole tumor tissue versus normal pancreatic tissue, in which COL11A1 (probe 37892_at) is again prominent and the top entry (log fold change 5.15) was INHBA, supportive of our hypothesis of activin A induced TGF-β signaling.
From these distributions, 282 probes were differentially expressed between the Per35/5 and WT mice, and 96 probes were differentially expressed between the Per34/4 and WT mice (Supplemental Fig. S1 A, see Supplemental Table S2 for top 30-fold change probes for each genotype).
If genes in a pathway rank at the top of the new fold change list, ie. they are overrepresented at the top, then the enrichment score (ES) will be close to 1. Conversely if the ES = −1, then genes are overrepresented at the bottom of our fold change data.
A positive NES indicates that the list of genes is enriched at the "top" of the ordered fold change list, and a negative NES indicates that the list in question is enriched at the "bottom" of the list.
