Table 2.

Transcriptional profile of healthy synovium and synovium at 4 weeks following the surgical induction of osteoarthritis. Non-mitochondrial, non-ribosomal protein coding genes with RPKM>2000 (see Supplementary Table 2 for full list).

Rank	Gene symbol *	Protein name	Intact RPKM **	Secreted ***
Healthy Synovium
1	DCN	Decorin	9165.4	Yes
2	APOR	Apolipoprotein R	8253.7	Yes
3	EF1ALPHA	Elongation factor 1-alpha 1	8239.9	-
4	UBC	Ubiquitin C	6830.0	-
5	MGP	Matrix Glaprotein	6133.0	Yes
6	FN1	Fibronectin	5739.8	Yes
7	CLU	Clusterin	4577.6	Yes
8	COL3A1	Collagen alpha-1(III) chain	3970.5	Yes
9	FTL	Ferritin light chain	3840.3	-
10	CST3	Cystatin-C	3567.2	Yes
11	FTH1	Ferritin heavy chain	3207.1	-
12	VIM	Vimentin	2948.8	Yes
13	S100A6	Protein S100-A6	2796.7	Yes
14	C1QC	Complement C1q subcomponent subunit C	2775.9	Yes
15	ENSSSCG00000004579	Uncharacterizedprotein	2729.1	-
16	PRG4	Proteoglycan 4	2502.1	Yes
17	TMSB10	Thymosin beta-10	2311.3	-
18	CTSB	Cathepsin B	2272.9	Yes
Synovium at 4W post-surgery
1	COL3A1	Collagen alpha-1(III) chain	12194.9	Yes
2	COL1A1	Collagen alpha-1(I) chain	6962.5	Yes
3	EF1ALPHA	Elongation factor 1-alpha 1	6205.8	-
4	FN1	Fibronectin	5488.4	Yes
5	UBC	Ubiquitin C	5352.5	-
6	DCN	Decorin	4084.1	Yes
7	SPARC	SPARC (Secreted protein acidic and rich in cysteine)	3832.4	Yes
8	FTH1	Ferritin heavy chain	3398.3	-
9	PRG4	Proteoglycan 4	3211.0	Yes
10	VIM	Vimentin	3093.6	Yes
11	SPARC ****	SPARC (Secreted protein acidic and rich in cysteine)	2990.2	Yes
12	COL1A2	Collagen alpha-2(I) chain	2963.0	Yes
13	ENSSSCG00000004579	Uncharacterizedprotein	2868.5	-
14	TMSB10	Thymosin beta-10	2817.0	-
15	CLU	Clusterin	2779.3	Yes
16	S100A6	Protein S100-A6	2518.4	Yes
17	FTL	Ferritin light chain	2507.1	-
18	APOR	Apolipoprotein R	2488.2	Yes
19	MGP	Matrix Glaprotein	2363.8	Yes

^*Ensemble identifier is provided when gene symbol is not available,

^**RPKM = reads per kilobase of transcript per million mapped reads,

^***Encoding secreted proteins based on annotations in the Uniprot database,

^****Orthologue.