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Table 1 Functional interpretation of genes associated with immobilization-induced knee joint contractures. The lists of genes included in all clusters identified for the sham-operated and for the immobilization group were compared for similarities. Genes associated with the immobilization intervention only were submitted to Gene Ontology (GO), KEGG Pathways, and Reactome Pathway analysis. Analyses were performed using default settings for terms of the GO Biological Processes (BP_FAT), GO Molecular Function categories (MF_FAT) and GO Cellular Component (CC_FAT) (not shown). Significant GO terms and pathways from KEGG and Reactome mapping are listed. The list of genes included in each enriched terms was compared to immobilization genes identified by clustering using CAGED application. Numbers in parenthesis indicate the number of common probe sets between enriched terms and CAGED clusters

From: Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures

GO Terms P-value CAGED cluster (# of probes in cluster) KEGG Pathways P-value CAGED cluster (# of probes in cluster) Reactome Pathways P-value CAGED cluster (# of probes in cluster)
Biological Process Dilated cardiomyopathy 4.8 x 10−4 1 (2) Muscle contraction 5.0 x 10−10 1 (3)
4 (3) 4 (3)
5 (4) 5 (4)
8 (1) 8 (1)
Extracellular structure organization 9.2 x 10−7 1 (5) ECM-receptor interaction 2.0 x 10−3 1 (2) Triglyceride biosynthesis 3.6 x 10−7 4 (9)
4 (4) 4 (1)
5 (1) 6 (3)
6 (2) 8 (1)
Lipid biosynthetic process 1.9 x 10−5 1 (3) Hypertrophic cardiomyopathy (HCM) 2.4 x 10−3 1 (2) Gelatin degradation by MMPs 3.8 x 10−7 1 (2)
4 (12) 4 (2) 4 (3)
5 (4) 6 (2)
8 (1)
Neutral lipid metabolic process 2.0 x 10−5 1 (1) Cardiac muscle contraction 1.1 x 10−2 4 (2) Collagen type XI degradation by MMPs 9.7 x 10−7 1 (2)
4 (8) 5 (4) 4 (2)
8 (1) 6 (1)
Cellular Component Focal adhesion 2.2 x 10−2 1 (3) Degradation of collagen 1.3 x 10−6 1 (2)
4 (1)
6 (3)    4 (5)
8 (1) 6 (2)
Extracellular region part 8.6 x 10−9 1 (7) Biosynthesis of unsaturated fatty acids 2.9 x 10−2 4 (3) Collagen type X degradation by MMPs 2.2 x 10−6 4 (2)
4 (15) 6 (1)
5 (1)
6 (4)
8 (1)
Extracellular matrix 2.0 x 10−8 1 (4) Complement and coagulation cascades 4.4 x 10−2 4 (3) ATP Hydrolysis by Myosin; Myosin Binds ATP; Calcium Binds Caldesmon; Release of ADP From Myosin 4.8 x 10−6 1 (3)
4 (9) 5 (1) 4 (1)
6 (4) 5 (2)
8 (1) 8 (1)
Proteinaceous extracellular matrix 2.2 x 10−8 1 (4) PPAR signalling pathway 4.5 x 10−2 4 (5) Degradation of the extracellular matrix 7.5 x 10−6 1 (1)
4 (8) 4 (5)
6 (4) 6 (2)
8 (1)
  Glycine, serine and threonine metabolism 5.0 x 10−2 1 (1) Smooth Muscle Contraction 7.9 x 10−6 1 (3)
4 (2) 4 (1)
5 (2)
8 (1)