Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression

Funari, Vincent A; Day, Allen; Krakow, Deborah; Cohn, Zachary A; Chen, Zugen; Nelson, Stanley F; Cohn, Daniel H

doi:10.1186/1471-2164-8-165

BMC Genomics

Table 1 Cartilage-selective genes validated in silico on U133A (left), U133B (center), and U133 Plus 2.0 (right) platforms.

From: Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression

U133A SYMBOL	Probe	CV	Class	Mouse	Human	SAM	Fold	U133B SYMBOL	Probe	CV	Class	Mouse	Human	SAM	Fold	U133 2.0 SYMBOL	Probe	CV	Class	SAM	Fold
AGC1	207692_s_at	9.0	ST		x	14	65.6	COL11A1	229271_x_at	11.0	ST	x	x	3	54.2	FLJ16008	1568868_at	6.4		44	8.2
AGC1	217161_x_at	9.2	ST		x	31	15.5	230895_at	230895_at	11.3				4	67.0	UBE3C	1560739_a_at	8.5	EZ	305	5.1
MATN1	206905_s_at	9.6	ST			22	75.3	EDIL3	233668_at	11.8	SI			221	6.0	1563414_at	1563414_at	8.8		77	5.1
COL10A1	217428_s_at	9.9	ST	x	x	284	5.9	C10orf49	236800_at	15.5				13	76.0	IRAK2	1553740_a_at	11.0	SI	107	6.3
MATN3	206091_at	10.1	ST		x	32	6.7	IRAK2	231779_at	15.6	SI			158	25.1	COL25A1	1555253_at	11.4	ST	516	5.1
MMP13	205959_at	10.2	ME	x	x	6	28.9	SLC4A5	234976_x_at	16.3	EZ			1036	6.4	KIAA0701	1554292_a_at	11.6		57	5.9
MATN4	207123_s_at	10.4	ST			59	7.8	LOC399959	239672_at	16.4				633	10.2	SULT1C2	1553321_a_at	11.7	ME	105	7.5
AGC1	205679_x_at	10.6	ST		x	18	28.6	IBSP	236028_at	16.4	SI			628	19.0	ITGB1	1561042_at	11.7	SI	542	7.0
COL11A2	216993_s_at	11.5	ST	x	x	116	7.3	EDNRA	243555_at	22.0	SI	x		213	5.6	RP4-756G23.1	1557123_a_at	13.1		214	6.2
NOS2A	210037_s_at	11.6	SI			20	18.7	HSUP1	229899_s_at	22.2				1994	5.1	NRP2	1555468_at	13.7	SI	45	10.2
LECT1	206309_at	13.3	SI	x		34	52.3	COL9A2	232542_at	22.5	ST		x	1929	5.0	MSI2	1552364_s_at	14.2	SI	178	5.2
HAS2	206432_at	14.2	ME			91	5.4	CMAH	229604_at	23.0	EZ			272	8.0	PTGFR	1555097_a_at	17.0	SI	470	8.0
WISP1	206796_at	15.6	SI			15	7.1	SNX5	223666_at	23.1	SI			108	5.3	BCL10	1557257_at	17.5	EZ	1014	6.1
HAPLN1	205523_at	18.5	ST	x		8	18.8	EDG2	232716_at	23.2	SI	x		712	5.4	WTAP	1560274_at	17.5	SI	228	6.3
COL9A1	222008_at	19.4	ST	x	x	19	185.1	TNFRSF18	224553_s_at	23.9	SI			124	9.4	RUNX1	1557527_at	17.8	SI	297	13.0
C1QTNF3	220988_s_at	20.3				291	5.4	USP12	236975_at	23.9	EZ			1776	6.3	LACTB	1552485_at	18.6	EZ	659	6.5
COL11A2	213870_at	20.5	ST	x	x	11	136.9	RP6-213H19.1	224407_s_at	25.3	SI			313	5.8	WWP2	1552737_s_at	21.1	EZ	144	10.9
COL10A1	205941_s_at	20.5	ST	x	x	684	38.5	BIC	229437_at	26.9	SI			571	5.5	PITPNC1	1568949_at	21.5	SI	258	5.5
NGFB	206814_at	21.0	SI			78	7.1	KIAA1718	225142_at	27.8				651	11.5	ARIH1	1558710_at	22.2	EZ	1264	5.2
PDPN	204879_at	21.5	ST	x		103	8.8	RB1CC1	237626_at	27.9	SI			1489	5.5	ADAMTS9	1554697_at	22.7	ME	769	7.4
222348_at	222348_at	21.8				227	8.4	WTAP	244219_at	28.1	SI			371	6.1	SYNJ2	1555009_a_at	23.7	SI	277	5.9
SLC28A3	220475_at	21.9	SI			296	5.1	RHOQ	239258_at	28.2	SI			784	5.4	SRGAP1	1554473_at	23.8	SI	809	5.1
EIF2C2	213310_at	22.4	EZ			1071	9.1	RPS6KA3	241460_at	28.3	SI	x	x	529	9.1	MGC17337	1552277_a_at	24.2		690	6.0
SOX5	207336_at	23.5	SI	x		1250	8.2	SEMA6D	233801_s_at	29.1	SI			245	5.3	1555841_at	1555841_at	24.5		1606	6.8
DSPG3	206439_at	24.0	ME			5	15.0	FN1	235629_at	29.6	ST			622	10.5	CD44	1565868_at	24.8	SI	1025	6.2
COL11A1	37892_at	25.7	ST	x	x	12	82.4	ULBP2	238542_at	29.7	SI			101	6.1	SLC41A2	1562208_a_at	24.9	ST	407	8.7
COL11A1	204320_at	26.0	ST	x	x	73	63.6	229221_at	229221_at	30.1				176	7.6	RHOF	1554539_a_at	26.7	SI	704	6.4
SOD2	215078_at	26.2	EZ			76	10.7	PTK2	241453_at	30.2	SI			355	7.7	ARF1	1565651_at	27.7	SI	768	5.6
HSPC159	219998_at	27.6	EZ			126	8.1	CHST11	226368_at	30.6	ME			310	5.3	1552288_at	1552288_at	28.0		127	17.1
BMP2	205289_at	29.3	SI			591	17.4	VASN	225867_at	31.9	SI			593	5.9	B3GNT5	1554835_a_at	29.5	ME	331	5.5
CSPG4	214297_at	29.5	ST			17	39.5	SCUBE3	230290_at	33.3	SI			123	6.4	B3GNT7	1555963_x_at	30.4	ME	339	18.3
CHST3	32094_at	30.0	EZ		x	1560	6.3	LOC338758	238893_at	33.4				998	5.2	SETD5	1569106_s_at	31.2		839	6.0
RELB	205205_at	30.1	SI			390	7.7	LOXL4	227145_at	33.8	EZ			260	7.5	OSMR	1554008_at	31.9	SI	85	50.3
CYTL1	219837_s_at	30.7	SI			151	17.0	SLC25A37	242335_at	33.9	SI			765	12.3	ZFYVE16	1554638_at	32.2		722	5.2
FZD10	219764_at	30.8	SI			51	7.3	228910_at	228910_at	34.0				630	5.4	AKR1C2	1562102_at	32.8	EZ	559	5.7
BDKRB1	207510_at	31.6	SI			239	5.1	PITPNC1	239808_at	34.3	SI			1129	11.8	WTAP	1558783_at	33.2	SI	946	8.0
ITGA10	206766_at	32.6	SI	x		41	29.4	FNDC3B	222693_at	34.3	SI			1394	10.2	LRRC8C	1558517_s_at	33.4		731	5.3
RNF24	210706_s_at	32.6				774	5.1	PDPN	226658_at	35.2	ST			125	15.7	1552289_a_at	1552289_a_at	34.4		164	28.5
NUPL1	204435_at	33.0	SI			1680	5.2	LOC201181	241383_at	35.2				173	14.5	SFXN3	1559993_at	35.7	SI	160	7.8
RNF24	204669_s_at	33.0				1349	6.0	FNDC3B	244022_at	37.0	SI			456	7.3	LRP11	1561180_at	37.8	SI	393	10.3
AKR1C2	217626_at	33.6	EZ			595	12.3	CHST11	226372_at	37.9	ME			554	5.9	B3GNT7	1555962_at	38.2	ME	396	12.5
LOC283824	213725_x_at	35.5				1433	6.5	225611_at	225611_at	38.2				1117	7.4	ZNF146	1569312_at	38.3		374	10.5
PDLIM4	214175_x_at	35.6	SI			212	5.6	NRP2	232701_at	38.6	SI			58	6.5	ZCCHC7	1556543_at	41.5		1906	6.2
FOSL1	204420_at	37.8	SI		x	458	15.2	TNFRSF10D	227345_at	38.7	SI			363	6.5	ATF1	1565269_s_at	42.0	SI	533	6.7
HAPLN1	205524_s_at	38.4	ST	x		16	137.6	FNDC3B	232472_at	39.4	SI			327	5.9	HIG2	1554452_a_at	43.0	EZ	119	44.6
MIA	206560_s_at	41.0	ST	x		36	8.1	229242_at	229242_at	39.7				330	6.3	KLF7	1555420_a_at	43.3	SI	1056	5.7
MMP12	204580_at	41.3	ME			29	8.2	ANKRD28	229307_at	39.7	SI			820	7.6	BCL2L11	1558143_a_at	43.8	EZ	683	6.2
TNMD	220065_at	41.9	ST	x		113	5.0	TRPS1	234351_x_at	39.7	SI		x	841	5.6	TGIF	1566901_at	43.8	SI	380	6.1
RLF	204243_at	43.0	SI			478	7.8	GLIS3	230258_at	40.2	SI			872	5.4	MCOLN2	1555465_at	43.9		520	8.6
EDIL3	207379_at	44.2	SI			84	5.4	SCUBE3	228407_at	40.2	SI			515	5.9	ChGn	1569387_at	44.7	ME	843	5.4
THBS3	209561_at	45.0	SI	x		716	7.2	SCYL1BP1	226337_at	40.5				1714	6.9	PTK2	1559529_at	45.1	SI	562	6.2
MMP3	205828_at	46.6	EZ	x		1	73.5	YME1L1	232216_at	40.9	ME			2251	5.5	FAM62B	1555830_s_at	49.5		837	6.6
RELA	209878_s_at	47.1	SI			971	7.3	KIAA0999	242920_at	41.0				1731	8.4
LIF	205266_at	47.9	SI			120	15.7	236289_at	236289_at	41.2				445	5.4
BMP6	206176_at	48.3	SI	x		60	38.9	GALNTL2	236361_at	42.1	ME			290	15.7
ETNK1	219017_at	49.0	EZ			1400	5.1	PET112L	228441_s_at	42.2	EZ			333	9.8
								ZNF697	227080_at	42.2				1119	5.5
								FNDC3B	222692_s_at	42.3	SI			747	9.4
								GPC6	223730_at	42.4	SI			511	9.5
								COL27A1	225292_at	42.7	ST			135	5.4
								NRP2	229225_at	43.1	SI			96	9.8
								UFM1	242669_at	44.1	EZ			624	6.6
								ASAM	228082_at	44.3	SI			68	11.7
								KCNT2	234103_at	44.4	EZ			299	5.3
								ERO1L	222646_s_at	44.6	EZ			1358	6.8
								MAST4	225613_at	44.6	SI			642	7.9
								228314_at	228314_at	44.7				1501	6.5
								C8orf72	232668_at	45.0				400	15.6
								RPS6	238156_at	45.7	EZ			1922	5.1
								SQSTM1	244804_at	46.6	EZ	x		1440	5.6
								230204_at	230204_at	46.8				26	78.1
								TBX15	230438_at	46.9	SI			932	5.9
								244533_at	244533_at	47.0				752	5.5
								235821_at	235821_at	47.2				35	9.9
								ZNF160	239954_at	47.5				1897	7.1
								SERPINE2	236599_at	47.9	EZ			80	12.1
								236685_at	236685_at	49.5				1555	5.5

Genes were ranked by selectivity (CV) and classified into four functional classes Structural Protein (ST), Enzyme (EZ), Signaling (SI), and Extracellular Matrix Enzyme (ME). Genes associated with skeletal phenotypes in mice and/or human or genes are denoted in Mouse and Human columns, respectively. SAM defines the rank order of each gene identified by two-class SAM analysis of cartilage versus non-cartilage tissues. The average cartilage expression divided by the median of non-cartilage expression (Fold) is listed for each gene.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com