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Table 2 SAM (significance analysis of microarrays) analysis of genes correlated to percentage tumour content.

From: The effect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis

Gene name Genbank accession Unigene cluster ID Symbol Score (d) q-value (%)
ADP-ribosylation factor 1 AK023803 Hs.286221 ARF1 3.11 4.13
CDC28 protein kinase regulatory subunit 2 BQ898943 Hs.83758 CKS2 2.73 4.13
TRK-fused gene NM_006070 Hs.446568 TFG 2.65 4.13
Discs, large homolog 7 (Drosophila) NM_014750 Hs.77695 DLG7 2.60 4.13
RAB6B, member RAS oncogene family NM_016577 Hs.352530 RAB6B 2.59 4.13
Epithelial cell transforming sequence 2 oncogene AY376439 Hs.293257 ECT2 2.56 4.13
FXYD domain containing ion transport regulator 2 CR627143 Hs.413137 FXYD2 2.54 4.13
Ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila) NM_004652 Hs.77578 USP9X 2.48 4.13
Pitrilysin metalloproteinase 1 CR749279 Hs.528300 PITRM1 2.46 4.13
Myeloid differentiation primary response gene (88) AK124685 Hs.82116 MYD88 2.44 4.13
Baculoviral IAP repeat-containing 5 (survivin) NM_001012271 Hs.1578 BIRC5 2.42 4.13
Polo-like kinase 4 (Drosophila) NM_014264 Hs.172052 PLK4 2.40 4.13
2',3'-cyclic nucleotide 3' phosphodiesterase NM_033133 Hs.443836 CNP 2.40 4.13
Triosephosphate isomerase 1 BM913099 Hs.83848 TPI1 2.39 4.13
ALL1-fused gene from chromosome 1q BX649117 Hs.75823 AF1Q 2.37 4.13
Latent transforming growth factor beta binding protein 2 NM_000428 Hs.105689 LTBP2 -3.49 1.00
LIM domain binding 2 AL832772 Hs.4980 LDB2 -3.43 1.00
Collagen, type XV, alpha 1 NM_001855 Hs.409034 COL15A1 -3.39 1.00
Cadherin 5, type 2, VE-cadherin (vascular epithelium) NM_001795 Hs.76206 CDH5 -3.39 1.00
Forkhead box O1A (rhabdomyosarcoma) NM_002015 Hs.170133 FOXO1A -3.17 1.00
TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous) BC035514 Hs.89640 TEK -3.02 1.00
Regulator of G-protein signaling 5 NM_003617 Hs.24950 RGS5 -2.97 1.00
Fasciculation and elongation protein zeta 1 (zygin I) NM_022549 Hs.79226 FEZ1 -2.90 1.00
Vascular endothelial growth factor C NM_005429 Hs.79141 VEGFC -2.90 1.00
Tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain NM_003841 Hs.253829 TNFRSF10C -2.82 1.00
CDNA FLJ25106 fis, clone CBR01467 AK128814 Hs.432914   -2.79 1.00
Alpha-2-macroglobulin CR749334 Hs.74561 A2M -2.77 1.00
Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse) NM_170677 Hs.362805 MEIS2 -2.71 1.00
Tropomodulin 1 AK096156 Hs.404289 TMOD1 -2.70 1.00
Isoleucine-tRNA synthetase NM_013417 Hs.172801 IARS -2.63 1.00
  1. Positive values for score (bold) indicate positive correlation with percentage tumour, and negative values indicate inverse correlation with percentage tumour (underlined). The table has been truncated to show only genes with the lowest false discovery rates (q).