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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
  1. The pathways sub-lined were found in at least two of the three analyses.1 Biological process GO terms obtained by the Gene Ontology Tree Machine software (GOTM). Are only indicated the enriched biological process GO terms with a significant level of pvalue < 0.01 (see Methods) and a minimum of 3 genes associated. 2 Kegg pathways: are only indicated those with a minimum of 3 genes associated and having a probability to be observed in the cluster 4-fold superior than the probability to obtain it by chance.3 Ingenuity pathways: are indicated the top five Canonical pathways associated to each cluster (pvalue < 0.01). Only canonical pathways with at least 3 genes affiliated were conserved.