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

Table 1 Ontological classes of differentially expressed genes in early rheumatoid arthritis versus controls

	Gene regulation	Early rheumatoid arthritis versus controls	P value
Biological processes
	Up (cluster 2)
		Reverse transcription	0.007
		Amino acid activation	0.01
		Protein biosynthesis^a	0.02
		Nucleoside, nucleotide, and nucleic acid metabolism^a	0.02
		Protein metabolism and modification	0.03
		Other immune and defense	0.04
	Down (cluster 1)
		Granulocyte-mediated immunity	0.0004
		Other cell cycle process	0.01
		Macrophage-mediated immunity	0.02
		T cell-mediated immunity	0.03
		Other blood circulation and gas exchange activity	0.04
		Mitochondrial transport	0.05
Molecular functions
	Up (cluster 2)
		Ribosomal protein^a	0.005
		Reverse transcriptase	0.007
		Nucleic acid binding	0.009
		Other transcription factor	0.03
		Defense/immunity protein	0.03
		Nuclease	0.04
		Antibacterial response protein	0.05
	Down (cluster 1)
		Transmembrane receptor regulatory/adaptor protein	0.008
		Metalloprotease inhibitor^a	0.02
		Phosphorylase	0.03
		Protease inhibitor	0.03
		Cysteine protease inhibitor	0.04
Pathways
	Up (cluster 2)
		Bupropion degradation	0.007
		Salvage pyrimidine deoxyribonucleotides^a	0.01
	Down (cluster 1)
		Metabotropic glutamide receptor group I pathway	0.07

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 2).

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