OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets

Madden, Stephen F; Clarke, Colin; Stordal, Britta; Carey, Mark S; Broaddus, Russell; Gallagher, William M; Crown, John; Mills, Gordon B; Hennessy, Bryan T

doi:10.1186/1476-4598-13-241

Molecular Cancer

Table 1 Summary description of clinical datasets used by OvMark

From: OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets

GEO accession	Ref.	Sample number	Platform type (probe number)	Mean age ± SD (Years)	Residual tumour information	Treatment Information (Pl/Ta/Neo/ Chemo)	FIGO stage					Histology			Tumour grade				Mean survival ± SD (months)
GEO accession	Ref.	Sample number	Platform type (probe number)	Mean age ± SD (Years)	Residual tumour information	Treatment Information (Pl/Ta/Neo/ Chemo)	1	2	3	4	NA	Ser	End	NA	1	2	3	NA	DFS	OS
GSE26712	Bonome et al.[18]	185	Affymetrix U133A (~22 K)	×	Yes	×	×					×			×				×	47 ± 36
GSE13876	Crijns et al.[19]	157	Operon human v3 (~35 K)	58 ± 12	×	×	×					157	0	0	×				×	37 ± 40
GSE14764	Denkert et a l. [20]	80	Affymetrix U133A (~22 K)	×	Yes	×	8	1	69	2	0	62	6	12	3	23	54	0	×	34 ± 15
GSE30161	Ferris et al. [21]	58	Affymetrix U133Plus2 (~54 K)	63 ± 11	×	Pl/Neo/Chemo	×					47	1	10	×				24 ± 32	46 ± 36
GSE19161	Konstantinopoulos et al.[22]	61	Affymetrix 0.6 K Custom Chip (~600)	×	×	Pl/Ta	×					×			×				×	31 ± 19
GSE19829	Konstantinopoulos et al.[23]	70	Affymetrix U133Plus2 (~54 K) / Affymetrix U95v2 (~12 K)	×	×	×	×					×			×				×	39 ± 23
GSE26193	Mateescu et al. [24]	107	Affymetrix U133Plus2 (~54 K)	58 ± 11	Yes	×	×					83	8	16	7	32	68	0	50 ± 52	59 ± 51
TCGA	McLendon et al. [25, 26]	562	Affymetrix U133A (~22 K)	×	×	Chemo	×					×			×				×	33 ± 27
GSE18520	Mok et al. [27]	53	Affymetrix U133Plus2 (~54 K)	×	×	×	×					×			×				×	40 ± 41
GSE31245	Spentzos et al. [28]	57	Affymetrix U95v2 (~12 K)	×	×	×	×					×			×				×	42 ± 16
GSE9899	Tothill et al.[29]	285	Affymetrix U133Plus2 (~54 K)	60 ± 11	Yes	Pl/Ta/Neo	24	18	217	22	4	264	20	1	19	97	164	5	21 ± 18	31 ± 23
GSE17260	Yoshihara et al. [30]	110	Agilent- 4x44K (~41 K)	×	×	×	×					110	0	0	26	41	43	0	22 ± 18	36 ± 20
GSE32062	Yoshihara et al.[31]	260	Agilent- 4x44K (~41 K)	×	×	Pl/Ta	×					260	0	0	0	131	129	0	27 ± 23	45 ± 52
In-house	In-house Dataset	84	Affymetrix HuEx-1.0st v2	62 ± 12	Yes	Neo	4	11	56	11	0	80	1	3	7	16	61	0	19 ± 22	35 ± 26

Pl = Platinum, Ta = Taxane, Neo = Neoadjuvant Chemotherapy, Chemo = Chemotherapy, NA = Not Available, Ser = Serous, End = Endometrioid, DFS = Disease Free Survival, OS = Overall Survival, TCGA = The Cancer Genome Atlas, × = Missing Data, SD = Standard Deviation.

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ISSN: 1476-4598

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