Table 2.

Validation by quantitative RT-PCR

Gene designation		Groups compared	Fold change (RT-PCR)	Fold change (Microarray)	P value*
COL9A1	Collagen, type IX, alpha 1	CS > chordoma	407.5	118	0.03
COL9A1	Collagen, type IX, alpha 1	CS > STS	1549.6	93.2	0.03
HMW-MAA		CS > STS	3.87	3.87	0.03
HMW-MAA		Chordoma > STS	7.7	9.5	0.009
HMW-MAA		Chordoma = CS	2.0	NA**	0.14
CD24	CD24 antigen	Chordoma > CS	36.3	27.3	0.01
CD24	CD24 antigen	Chordoma > STS	50.6	26.5	0.009
T	T, Brachyury	Chordoma > CS	1072.9	228.1	0.03
T	T, Brachyury	Chordoma > STS	17157.3	79.7	0.03

^*P values are based on RT-PCR data for the respective groups compared;

^**NA HMW-MAA gene was not differentially expressed in chordoma and chondrosarcoma samples by microarray analysis