In addition, the MYB, NAC and DOF TFs were also predicted to be regulating PGM, while PK was predicted to be regulated by MYB.
Among the 1729 genes, 299 up-regulated and 330 down-regulated genes were predicted to be regulated by the 59 differentially expressed miRNAs (Additional files 5 and 6).
A total of 8,492 unique candidate target genes were predicted to be regulated by the 39 up-regulated (maturation- relative to secretory-stage) miRNAs.
Likewise, 6,518 unique candidate target genes were predicted to be regulated by the 20 down-regulated (maturation- relative to secretory-stage) miRNAs.
Using the microRNA target prediction tool Targetscan [ 11], 556 genes were predicted to be regulated by miR-4732-3p (Additional file 7: Table S6).
The expression of Cyclin D1, FOXP1, FIH-1, pan-ERβ, NRP1 and CD99, predicted to be regulated by BRCA1 specific miRNAs by computer prediction algorithms, was assessed via immunohistochemistry in a cohort of 35 BRCandand 52 sporadic basal-like cancers.
For each miRNA predicted to be regulated by TDP-43, miRNA associated diseases were collected from the miR2Disease database (Jiang et al., 2009).
Subcluster 3 is composed of many interferon regulated genes, and is predicted to be regulated by Irf4 and Nr2f6.
Given the lack of intrinsic GTPase activity of ArfA, its activity is predicted to be regulated by GAPs.
Several genes that are predicted to be regulated by these microRNAs are shown in Table 2 and include Grb10, Lmna, Peg10, and Trp53.
This novel motif was found in about one third of the human 3'-UTRs of transcripts that are predicted to be regulated by miRNAs.
