Maximizing biomarker discovery by minimizing gene signatures

BMC Genomics

Table 3 Biological associations between genes and breast cancer

Gene	General description	Support	Endpoint D		Endpoint E
			Overlap	Position	Overlap	Position
CA12	Highly correlated with Erα	+	67	-5	61	4
MAPT	prognostic values in ER(+) Primary breast cancers in 3 patient cohorts	+	43	-7	22	26
ESR1	Involved in pathological processes of breast cancer	+	33	-2	53	1
GATA3	A breast cancer marker	+	25	-14	40	6
BTG3	Protein coding		22	75		-142
NFIB	Differentially expressed reported [39]		22	84	20	-61
LDHB	Protein coding		21	27		-239
RARRES1	Downregulated reported [40]		20	2	19	-2
CCND1	Aberrantly regulated and could contribute to therapeutic failure in the context of ER-positive breast cancer	+	18	-56		145
ELF5	Downregulated reported [41]		16	7		-16
IL6ST	Protein coding			-60	33	60
SLC39A6	Coregulated with estrogen receptor in some breast cancers	+		-64	25	41
TBC1D9	Protein coding			-25	25	19
ABAT	Protein coding			-34	16	29

Genes marked '+' indicates experimental support for a role in breast cancer in Support. Unless otherwise stated, descriptions were collected from Entrez Gene [25]. Numbers in the Overlap reflect number of gene overlap, for the top 10 ranked genes of two endpoints. Values for Position reflect these genes' rank in the descending sorted list of fold-change values, signs of which represent gene positions in the two ends of the list. Almost all top 10 genes for each endpoint rank in the top 200 up-regulated or down-regulated genes. Furthermore, among the genes common to these two endpoints, the change in expression level was not always correlated. In other words, genes up-regulated in endpoint D could be down-regulated in endpoint E.

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