Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia

Table 2 Ontological classes of differentially expressed genes in long-standing rheumatoid arthritis versus controls

	Gene regulation	Long-standing rheumatoid arthritis versus controls	P value
Biological processes
	Up (cluster 2)
		Pheromone response	0.002
		Chemosensory perception	0.002
		Pyrimidine metabolism	0.03
	Down (cluster 1)
		Fatty acid beta oxidation	0.003
		Protein biosynthesis^a	0.007
		Nucleoside, nucleotide, and nucleic acid metabolism^a	0.009
		Constitutive exocytosis	0.02
		Vitamin biosynthesis	0.03
		Amino acid transport	0.04
		Fatty acid metabolism	0.04
Molecular functions
	Up (cluster 2)
		Serine protease	0.003
		Interleukin receptor	0.02
		Protease	0.03
		Nucleotide kinase	0.04
		Cytokine receptor	0.04
	Down (cluster 1)
		Storage protein	0.002
		Ribosomal protein^a	0.01
		Metalloprotease inhibitor^a	0.02
		Amino acid transporter	0.02
		Extracellular matrix linker protein	0.02
		Other receptor	0.04
Pathways
	Up (cluster 2)
		Salvage pyrimidine deoxyribonucleotides^a	0.003
		Vasopressin synthesis	0.005
		p38 MAPK pathway	0.03
	Down (cluster 1)
		Vitamin D metabolism and pathway	0.02
		Histamine receptor-mediated signaling pathway	0.04
		Enkephalin release	0.04

The gene-ontology terms used are those of the PANTHER (Protein ANalysis THrough Evolutionary Relationships) database. ^aCommon ontological classes found in both comparisons: early rheumatoid arthritis (RA) or long-standing RA versus controls (see also Table 1). MAPK, mitogen-activated protein kinase.

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