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Table 1 Circadian pathways and associated cluster numbers.

From: Circadian signatures in rat liver: from gene expression to pathways

Pathway name Cluster ID
ASCORBATE AND ALDARATE METABOLISM 1
BUTANOATE METABOLISM 1
PURINE METABOLISM 1
LIMONENE AND PINENE DEGRADATION 1
DNA POLYMERASE 1
ATP SYNTHESIS 1
DNA REPLICATION REACTOME 1
LYSINE DEGRADATION 1
HISTIDINE METABOLISM 1
PHENYLALANINE METABOLISM 1
3 CHLOROACRYLIC ACID DEGRADATION 1
G1 TO S CELL CYCLE REACTOME 2
FATTY ACID METABOLISM 2
BILE ACID BIOSYNTHESIS 2
UREA CYCLE AND METABOLISM OF AMINO GROUPS 2
VALINE LEUCINE AND ISOLEUCINE DEGRADATION 2
TRYPTOPHAN METABOLISM 2
P53 SIGNALING PATHWAY 2
CELL CYCLE KEGG 2
G2 PATHWAY 2
ARGININE AND PROLINE METABOLISM 2
RNA POLYMERASE 2
IFNA PATHWAY 2
ST TYPE I INTERFERON PATHWAY 2
POLYUNSATURATED FATTY ACID BIOSYNTHESIS 3
CELL COMMUNICATION 3
ANTIGEN PROCESSING AND PRESENTATION 3
MRP PATHWAY 3
FRUCTOSE AND MANNOSE METABOLISM 3
TYROSINE METABOLISM 3
ETC PATHWAY 4
TYROSINE METABOLISM 4
MALATEX PATHWAY 4
PROTEASOME PATHWAY 4
ALANINE AND ASPARTATE METABOLISM 4
GLYCOLYSIS AND GLUCONEOGENESIS 4
SA CASPASE CASCADE 4
CHOLESTEROL BIOSYNTHESIS 5
GLYCEROPHOSPHOLIPID METABOLISM 5
TERPENOID BIOSYNTHESIS 5
RNA TRANSCRIPTION REACTOME 5
BIOSYNTHESIS OF STEROIDS 5
CIRCADIAN EXERCISE 5
CYANOAMINO ACID METABOLISM 5
FEEDER PATHWAY 5
GLYCEROLIPID METABOLISM 5
GLYCINE SERINE AND THREONINE METABOLISM 5
METHIONINE METABOLISM 5
LYSINE BIOSYNTHESIS 5
NUCLEOTIDE SUGARS METABOLISM 5
ETHER LIPID METABOLISM 5
SPHINGOLIPID METABOLISM 5
ONE CARBON POOL BY FOLATE 5
BASAL TRANSCRIPTION FACTORS 5
CIRCADIAN RHYTHM 5
LYSINE BIOSYNTHESIS 5
LYSINE DEGRADATION 5
MEF2 D PATHWAY 5
METHANE METABOLISM 5
METHIONINE METABOLISM 5
METHIONINE PATHWAY 5
ONE CARBON POOL BY FOLATE 5
SA G1 AND S PHASES 5
SELENOAMINO ACID METABOLISM 5
TID PATHWAY 5
TOLL PATHWAY 5
APOPTOSIS 5
APOPTOSIS GENMAPP 5
CARM ER PATHWAY 5
EPONFKB PATHWAY 5
FXR PATHWAY 5
G1 PATHWAY 5
GSK3 PATHWAY 5
LEPTIN PATHWAY 5
P53 PATHWAY 5
RACCYCD PATHWAY 5
SA REG CASCADE OF CYCLIN EXPR 5
TALL1 PATHWAY 5
  1. *) Since gene products can function in multiple pathways, some pathways that may not be active in liver can be identified as circadian. For example small cell lung cancer, SNARE interactions in vesicular transport, prion disease are not defined in liver tissue. For the statistical analysis, we are not biased by the tissue specific pathways; however an additional filtering is performed for the biologically relevant pathways.