Table 2.
Target gene prediction analysis on certain microRNAs found in common between ZEN medium and ZEN high groups, but significantly up- or down-regulated compared to control group.
| Homolog microRNAs in humans for target gene prediction analysisa | Number of predicted target genes found: | |||
|---|---|---|---|---|
| With scoring methodb | After filtering score > 17.0 | In common in the prediction datasets of at least two microRNAs, and enrichment pathway analysisc | In common in the prediction datasets of at least three microRNAs, and gene name | |
| Up-regulated microRNAs d | ||||
| hsa-miR-542-3p | 574 | 168 |
346 • Regulation gene expression: 137/346 (e.g. RNA polymerase II transcription) • Regulation signal transduction: 101/346 (e.g. signaling in cancer, by BMP, by WNT) • Regulation of protein modification process: 110/346 (e.g. SUMOylation) • Immune system: 69/346 (e.g. signaling by interleukins) |
42 SPRED1, C1orf21, MOB4, CACUL1, PLAG1, SOCS6, CAPZA2, ASH1L, SALL1, UBN2, CBX4, CD2AP, SREK1, BZW1, SKI, TAOK1, RAB9B, NUFIP2, SLIT2, RAPH1, FBXW7, PTPN4, HELZ, COPS2, CCND2, AGO1, RTN4, ARMC8, OCRL, KIF5B, EPB41L1, ZNF367, HNRNPA1, CREBL2, TSC22D2, CRK, RAB3IP, ZBTB43, AKIRIN1, ZDHHC15, MAP3K7, GLP2R |
| hsa-miR-424-5p | 1858 | 1054 | ||
| hsa-miR-503-5p | 416 | 254 | ||
| hsa-miR-450a-5p | 90 | 18 | ||
| hsa-miR-450b-5p | 2180 | 1051 | ||
| Down-regulated microRNAs d | ||||
| hsa-miR-181c-5p | 1135 | 410 |
65 • Disease of signal transduction: 17/65 (e.g. signaling by GPCR) |
5 THRB, SIRT1, MBNL1, PRLR, HIPK3 |
| hsa-miR-187-3p | 498 | 31 | ||
| hsa-miR-204-5p | 786 | 261 | ||
| hsa-miR-135a-5p | 939 | 481 | ||
The up-regulated microRNAs reported in this table belong to the same cluster (miR-503 in humans).
aSequences of mature microRNAs were compared between pigs and humans, and all of them have 100% homology on the seed sequence, and on the rest of the sequence as well (except 1 nucleotide change for miR-503-5p). bScoring method is based on prediction and occurrence scores for different databases (microT-CDS, TargetScan, miRDB, miRTarBase), and described in detail in the material and methods section. Further network prediction analysis can be found in Supplementary Fig. S3. cEnrichment pathway analysis were performed with Gene Ontology Consortium, and Reactome Pathway Database. dThe target gene prediction analysis was carried out only with microRNAs showing at least fold changes >3 or < −3 between ZEN high and Control.