Table 2.
Top five canonical pathways enriched by genes differentially expressed in response to photoperiod, time relative to parturition and the interaction
| Effect | Canonical Pathway | B-H P Value | Ratio | Differentially Expressed Genes |
|---|---|---|---|---|
| Photoperiod | cytotoxic T lymphocyte mediated apoptosis of cells | 0.008 | 0.034 | ↓BoLA, ↑BoLA-DQA5, BoLA-DRB3 |
| OX40 signaling | 0.010 | 0.031 | ↓BoLA, ↑BoLA-DQA5, BoLA-DRB3 | |
| B cell development | 0.036 | 0.056 | ↑BoLA-DQA5, BoLA-DRB3 | |
| antigen presentation | 0.055 | 0.048 | ↓BoLA, ↑BoLA-DQA5 | |
| fatty acid beta oxidation I | 0.059 | 0.044 | ↑SDS, ↓SLC27A6 | |
| Time | acute phase response signaling | < 0.0001 | 0.043 | ↑C3, C4BPA, CFB, CP, HP, IL6, IL33, LBP, RBP1 |
| LXR/RXR activation | 0.004 | 0.043 | ↑C3, CD14, IL6, IL33, LBP, LPL | |
| VDR/RXR activation | 0.004 | 0.057 | ↓CAMP, CXCL10, ↑CD14, IGFBP5, THBD | |
| granulocyte adhesion and diapedesis | 0.016 | 0.033 | ↓CXCL10, CXCL13, CLDN1, ↑IL33, SDC2, CXCL2 | |
| IL-10 | 0.019 | 0.051 | ↓CAMP, CXCL10, ↑CD14, IGFBP5, THBD | |
| Interaction | IGF-I signaling | 0.014 | 0.103 | ↑NOV, SOCS1, ↓FOS, IGF1R, JUN, KRAS, NEDD4, PRKACB, PRKAR2B, PTK2, YWHAG |
| CDK5 signaling | 0.064* | 0.093 | ↓ITGA2, KRAS, PPM1L, PPP1CB, PRKACB, PRKAR2B ↑ADCY3, PPP1R10, PPP1R3C | |
| dopamine receptor signaling | 0.077* | 0.083 | ↓PPM1L, PPP1CB, PRKACB, PRKAR2B ↑ADCY3, GCH1, PPP1R10, PPP1R3C | |
| sertoli cell junction signaling | 0.077* | 0.051 | ↓ACTN4, ATF2, CDH1, CLDN1, ITGA2 JUN, KRAS, PRKACB, PRKAR2B, PVRL3, SPTBN1 ↑ACTA1, ACTG2, TGFB3 | |
| protein kinase A signaling | 0.09* | 0.051 | ↓PPP1R3C, ADCY3, PPP1R10, TGFB3, HIST1H1C, TTN, PYGM,↑PRKACB, PPP1CB, PDE1A, AKAP5, DUSP10, PRKAR2B, ATF2, TGFBR1, YWHAG, BRAF, PTK2, EYA3, PTPLA, PTPN2 |
Biopsies were obtained from cows exposed to either long or short day photoperiod on days −24 and −9 relative to parturition. Microarray analysis was conducted on purified RNA using Affymetrix GeneChip Bovine Genome Arrays. Genes were identified in the effect of photoperiod treatment, time relative to parturition and the interaction. Differential expression was attributed to genes meeting the criteria of P ≤ 0.05 and fold-change ≥ |1.5|. IPA was used to identify canonical pathways. Benjamini-Hochberg (B-H) P value test correction to identify the probability of gene associations by chance (6). Ratio of differentially expressed genes to the total number of genes in the canonical pathway as defined by IPA.
Canonical pathways that did not meet the B-H threshold criteria of P ≤ 0.5. ↓Negative fold-change; ↑positive fold-change, within respective comparisons.