Table 1 Annotation of gene clusters using Gene Ontology (GO), KEGG and Ingenuity databases
From: Transcriptome profiling of the feeding-to-fasting transition in chicken liver
Biological process GO terms1 | KEGG pathways2 | Ingenuity pathways3 | |
|---|---|---|---|
Cluster 1 | Lipid metabolism SLC27A4 -LYPLA2-ENPP6-DGAT2L4-CYP51A1-FASN-SULT4A1-CPNE7-ANGPTL3-ACACA-LSS-ACLY-PBX1-PIGH-PLCL1-PRKAG3-PRKAA2-SCD -SBF2-PLA2G12B-MTMR3-PITPNM1 P = 5.E-04 | Fatty acid biosynthesis ACLY-FASN-ACACA-SCD | Fatty Acid Biosynthesis FASN-ACACA-MCCC2 P = 5.E-04 |
277 genes | Lipid biosynthesis DGAT2L4-CYP51A1-FASN-ACACA-LSS-ACLY-PBX1-PIGH-PRKAG3-PRKAA2-SCD P = 2.E-03 Fatty acid biosynthesis FASN-ACACA-PRKAG3-PRKAA2-SCD P = 6.E-03 Regulation of action potential KCNMB2-SBF2-EIF2B4 P = 7.E-03 | ||
Cluster 2 95 genes | Lipid metabolism PECI-DCTN6-CPT1A-FABP1-ACSL1-ACAA1-HADHA-HMGCS1-APOB-ACOX1-SCP2-ADIPOR2-PLCZ1 P = 3.E-06 Fatty acid metabolism PECI-CPT1A-FABP1-ACSL1-ACAA1-HADHA-ACOX1-ADIPOR2 P = 2.E-07 Fatty acid oxidation CPT1A-HADHA-ACOX1-ADIPOR2 P = 4.E-06 Fatty acid beta-oxidation CPT1A-HADHA-ACOX1 P = 2.E-05 Energy derivation by oxidation of organic compounds FBP1-IDH1-PCK1-FBP2-GYG2 P = 8.E-03 Gluconeogenesis FBP1-PCK1-FBP2 P = 4.E-04 | Fatty acid metabolism ACAT1-PECI-ACAA1-ACOX1-HADHA-ACSL1 PPAR signalling pathway PCK1-SCP2-FABP1-ACAA1-ACOX1-ACSL1 Synthesis and degradation of ketone bodies ACAT1-HMGCL-ACAA1-HMGCS1 Citrate cycle TCA cycle PCK1-ACAT1-HMGCL-IDH1-ACAA1 Gluconeogenesis PCK1-ACAT1-HMGCL-FBP1 Valine.leucine and isoleucine degradation ACAT1-HMGCL-ACAA1-HADHA-HMGCS1 Lysine degradation ACAT1-BBOX1-HADHA | Fatty Acid Metabolism CYP3A43-CYP4A22-CPT1A-ACAA1-CYP2C18-ACOX1-PECI-ACAT1-ACSL1-HADHA P = 2.E-11 Synthesis and Degradation of Ketone Bodies 1-06E01 6-42E-02 CYP3A43-CYP4A22-CPT1A-ACAA1-CYP2C18-ACOX1-PECI-CPT2-ACAT1-EHHADH-ACSL1-HADHA ACAA1-ACAT1-HMGCL-HMGCS1-HADHA P = 2.E-11 Pyruvate Metabolism ACAA1-ACAT1-PCK1-ACSL1-HADHA P = 2.E-05 Valine- Leucine and Isoleucine Degradation ACAA1-ACAT1-HMGCL-HMGCS1-HADHA P = 9.E-08 6-94E00 6-54E-02 ACAA1-ACAT1-HMGCL-HMGCS2-EHHADH-HMGCS1-HADHA Lysine Degradation BBOX1-ACAA1-ACAT1-MLL3-HADHA P = 1.E-06 Tryptophan Metabolism CYP3A43-CYP4A22-ACAA1-CYP2C18-ACAT1-HADHA P = 8.E-06 Propanoate Metabolism ACAA1-ACAT1-ACSL1-HADHA P = 1.E-05 1-36E00 2-02E-02 EHHADH-HADHA 8-54E-01 1-69E-02 PCK1-IGFBP1 |
Cluster 3 517 genes | Cell cycl e MPHOSPH9-TRIM13-TADA3L-YWHAQ-ESCO2-DBC1-E2F6-ERN1-FGF6-SH3BP4-FRAP1-GAS2-APBB2-KRAS-MAD2L1-MDM2-MLH1-MUTYH-NRAS-NDE1-PPP1CB-CDC37L1-PBK-PRKG2-PTMS-BARD1-CLSPN-NEK4-YWHAH-MAD1L1-MCM8-CCNH-PRC1-MTSS1-CUL7-DCLRE1A-CDC34 P = 9.E-03 Glycolysis DLAT-ENO1-OGDH-PGAM1-PKM2-UEVLD P = 8.E-03 Cytokinesis CECR2-PRC1-ROCK2 P = 7.E-03 Ceramide metabolism GALC-PRKAA1-SGPL1 P = 7.E-03 Regulation of protein catabolism ATE1-MDM2-BARD1 P = 2.E-03 | Insulin signalling pathway PTPN1-PRKAA1-KRAS-FRAP1-PRKAB1-SORBS1-CRK-NRAS ErbB signalling pathway _ CAMK2A-JUN-KRAS-FRAP1-PAK7-SRC-CRK-NRAS- GnRH signalling pathway CAMK2A-ADCY3-JUN-KRAS-CACNA1C-SRC-NRAS Renal cell carcinoma _ JUN-SLC2A1-KRAS-PAK7-ARNT-CRK-NRAS-EGLN3 Tight junction _ JAM3-KRAS-CLDN16-SRC-MAGI1-NRAS-ACTB Glioma _ CAMK2A-KRAS-FRAP1-MDM2-NRAS | Chemokine Signaling ROCK2-SRC-PLCB4-CAMK2A-NRAS-JUN-MYL2-PPP1CB-KRAS P = 3.E-04 Ephrin Receptor Signaling MAP3K14-SRC-NRAS-CREB3-SOS2-KRAS-CRK-ROCK2-AKT1-SORBS1-EFNB1-ACP1-ARPC4-PRKAA1-PAK7-MAK P = 6.E-04 B Cell Receptor Signaling MAP3K14-FRAP1-AKT1-CAMK2A-NRAS-JUN-MAP3K7-CREB3-SOS2-PIK3AP1-KRAS P = 3.E-03 Estrogen Receptor Signaling SRC-PRKDC-CCNH-NRAS-SOS2-KRAS-GTF2A1-MED4-ESR2 P = 3.E-03 PDGF Signaling SRC-NRAS-JUN-ACP1-SOS2-KRAS-CRK P = 4.E-03 Wnt/Î 2 -catenin Signaling SRC-AKT1-WIF1-MAP3K7-WNT7B-FZD3-DKK2-MDM2 (includes EG:4193)-WNT5B-WNT2-SOX5 (includes EG:6660) P = 6.E-03 Actin Cytoskeleton Signaling ABI2-TIAM1-NRAS-MYL2-ACTB-SOS2-PPP1CB-KRAS-CRK-FGF6-ROCK2-ARPC4-PRKAA1-PAK7-MAK P = 6.E-03 JAK/Stat Signaling FRAP1-AKT1-NRAS-SOS2-PTPN1-KRAS P = 8.E-03 Hypoxia Signaling in the Cardiovascular System AKT1-JUN-COPS5-CREB3-MDM2 (includes EG:4193)-CDC34-UBE2I-ARNT P = 6.E-04 |
Cluster 4 273 genes | TGF.beta signalling pathway ACVR2A-PPP2R2A-RBL1 Complement and coagulation cascades F13A1-C8B-F8-PLAU Purine metabolism ADSL-ITPA-ATIC-POLR1B-POLR3G-POLR2C Gap junction CDC2-PDGFA-MAP2K2-GNAI1 RNA_polymerase POLR1B-POLR3G-POLR2C Histidine_metabolism ADSL-GAD1-ATIC Long.term depression RARB-CASP9-STK4-MAP2K2 Long.term_potentiation GRIN2B-GRIN2A-MAP2K2 | cAMP-mediated Signaling CNGA4-MAP2K2-GNAO1-GNAI1-HTR1A-RGS12-CNGA1-CHRM3-CHRM5 P = 1.E-03 1–69°00 6–67°-02 HDAC4-TGFB3-RBL1-SIN3A Ephrin Receptor Signaling GRIN2B-GRIN2A-MAP2K2-PDGFA-CXCL12-GNAO1-ITGA2-GNAI1-ARPC3-CDC2-ACVR2A P = 1.E-03 1–26°00 3–64°-02 SOX9-GNAO1-RARB-TGFB3-SFRP5-ACVR2A |