Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer

BMC Cancer

Table 7 Number of common genes between different gene signatures for breast cancer prognosis

	Wang's 76 genes	van 't Veer's 70 genes	Paik's 16 genes	Yu's 62 genes
Wang's 76 genes^a		CCNE2	No genes	No genes
van 't Veer's 70 genes^b	CNNE2		SCUBE2	AA962149
Paik's 16 genes^c	No genes	SCUBE2		BIRC5
Yu's 62 genes^a	No genes	AA962149	BIRC5
Sotiriou's 97 genes^a	PLK1, FEN1, CCNE2, GTSE1, KPNA2, MLF1IP, POLQ	MELK, CENPA, CCNE2, GMPS, DC13, PRC1, NUSAP1, KNTC2	MYBL2, BIRC5, STK6, MKI67, CCNB1	URCC6, FOXM1, DLG7, DKFZp686L20222, DC13, FLJ32241, HSP1CDC21, CDC2, KIF11, EXO1

^aAffymetrix HG-U133A Genechip
^bAgilent Hu25K microarray
^cNo genome-wide assessment; RT-PCR
To compare genes from various prognostic signatures for breast cancer, five gene signatures were selected, the 76-gene signature [8], the 70-gene signature [3], the 16-gene signature [25], the 62-gene signature [26], and the 97-gene signature [23]. Identity of genes was determined by BLAST program when gene signatures were derived from different platforms. Except for the 97-gene expression grade index [23], which showed an overlap with 5 to 16 genes with the other gene signatures, a maximum overlap of only 1 identical gene was found between the other gene signatures. The initially reported 3-gene overlap between the 76-gene and the 70-gene prognostic signatures [8]included genes with high similarity in sequences. In this study, only genes with an identical sequence in two signatures are considered overlapped based on results from BLAST program. Therefore, CCNE2 gene is the only common gene between the two signatures.

ISSN: 1471-2407