Table 2.

Genes that highly correlated with the sensitivity of 23 breast cancer cell lines to dasatinib

No.Gene description *Gene symbolS2N Scoret test (P)Correlation with IC50Modulated by dasatinib
Sensitive gene signature
1Jagged 1 (Alagille syndrome)JAG11.671.8E−06−0.59Decreased
2Uridine phosphorylase 1UPP11.641.6E−04−0.45
3Polymerase I and transcript release factorPTRF1.584.3E−05−0.48Decreased
4Parvin, αPARVA1.584.8E−06−0.76
5Leprecan-like 1LEPREL11.568.0E−05−0.52
6IFN, γ-inducible protein 16IFI161.546.8E−06−0.54Increased
7Snail homologue 2 (Drosophila)SNAI21.522.0E−05−0.62
8Caveolin 2CAV21.473.5E−05−0.48Decreased
9Coagulation factor III (thromboplastin, tissue factor)F31.383.2E−03−0.64
10Proteasome (prosome, macropain) subunit, β type, 8 (large multifunctional protease 7)PSMB81.331.0E−04−0.52
11227361_at1.39.9E−03−0.54
12Alkylglycerone phosphate synthaseAGPS1.38.1E−04−0.55Decreased
13MoesinMSN1.291.3E−04−0.43
14Aldo-keto reductase family 1, member C3 (3-α hydroxysteroid dehydrogenase, type II)AKR1C31.284.0E−05−0.68Increased
15tumor necrosis factor receptor superfamily, member 21TNFRSF211.285.7E−05−0.59
16Annexin A1ANXA11.248.8E−04−0.40Decreased
17Potassium channel tetramerization domain containing 12KCTD121.235.1E−03−0.45
18Ras-related C3 botulinum toxin substrate 2 (rho family, small GTP-binding protein Rac2)RAC21.26.7E−03−0.50
19Caveolin 1, caveolae protein, 22kDaCAV11.24.3E−04−0.49Decreased
20EPH receptor B2EPHB21.191.8E−05−0.61
21Nicotinamide N-methyltransferaseNNMT1.184.3E−03−0.48Increased
22La ribonucleoprotein domain family, member 6LARP61.171.3E−03−0.46
23Proteasome (prosome, macropain) subunit, β type 9 (large multifunctional protease 2)PSMB91.161.2E−04−0.51
24Follistatin-like 1FSTL11.141.7E−04−0.49
25Anthrax toxin receptor 2ANTXR21.143.0E−04−0.51
26Arginine/proline-rich coiled-coil 1RPRC11.133.1E−05−0.51
27Exostoses (multiple) 1EXT11.137.0E−03−0.47
28Coagulation factor II (thrombin) receptor–like 1F2RL11.126.4E−06−0.62
29Inositol polyphosphate-1-phosphataseINPP11.112.5E−03−0.57
30Dihydropyrimidine dehydrogenaseDPYD1.12.0E−03−0.47
31FXYD domain containing ion transport regulator 5FXYD51.11.8E−05−0.57
32LayilinLOC1439031.095.0E−03−0.53
33Similar to solute carrier family 16 (monocarboxylic acid transporters), member 14LOC3468871.092.9E−03−0.50
34Sterile α motif domain containing 9–likeSAMD9L1.071.8E−05−0.48
35Zinc finger proteinZNF5591.042.1E−05−0.48
36Transforming growth factor, β-induced (68 kDa)TGFBI1.011.7E−03−0.53
37KIAA1949KIAA19491.015.4E−03−0.46
38Prion protein (p27-30; Creutzfeld-Jakob disease, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia)PRNP1.011.3E−03−0.48
39Rho GTPase activating protein 29ARHGAP2911.6E−03−0.61Decreased
40Oncostatin M receptorOSMR0.992.1E−04−0.43
41Surfactant-associated protein F mRNA, partial sequence0.997.3E−03−0.42
42Retinoic acid–induced 14RAI140.983.3E−03−0.41
43Laminin, β3LAMB30.982.3E−03−0.58
44ELK3, ETS domain protein (SRF accessory protein 2)ELK30.989.2E−04−0.47
45Suppressor of cytokine signaling 5SOCS50.982.0E−03−0.48
46Caldesmon 1CALD10.972.9E−03−0.44
47BH-protocadherin (brain-heart)PCDH70.972.1E−03−0.64
48Epithelial protein lost in neoplasm βEPLIN0.961.2E−03−0.67Decreased
49Popeye domain containing 3POPDC30.963.0E−03−0.41
50Coactosin-like 1 (Dictyostelium)COTL10.966.2E−04−0.41Decreased
51Ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homologue, yeast)UBE2E30.951.9E−04−0.46
52Plasminogen activator, urokinasePLAU0.947.3E−03−0.49
53Epidermal growth factor receptorEGFR0.941.8E−03−0.56Decreased
54Receptor-interacting serine-threonine kinase 4RIPK40.944.2E−03−0.67
55Butyrophilin, subfamily 3, member A3/member A2BTN3A3/A20.932.9E−04−0.59Increased
56Tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)TFPI0.936.4E−03−0.41
57Met proto-oncogene (hepatocyte growth factor receptor)MET0.922.7E−04−0.51Decreased
58Guanylate-binding protein 3GBP30.925.8E−03−0.49
59SH3-domain kinase binding protein 1SH3KBP10.927.1E−04−0.42
60Suppression of tumorigenicity 5ST50.921.7E−03−0.50
61Interleukin 15 receptor, αIL15RA0.921.4E−03−0.44
62CalpastatinCAST0.915.6E−04−0.67
63Collagen, type V, α1COL5A10.96.6E−03−0.43
64Kinetochore-associated 2KNTC20.891.1E−03−0.40
65Dual-specificity phosphatase 10DUSP100.897.1E−04−0.53
66EPH receptor A2EPHA20.897.8E−05−0.58Decreased
67Small fragment nucleaseDKFZP566E1440.891.7E−03−0.51
68Butyrophilin, subfamily 3, member A2BTN3A20.895.1E−04−0.52
69v-yes-1 Yamaguchi sarcoma viral-related oncogene homologueLYN0.889.5E−03−0.42
70Myosin XMYO100.883.5E−03−0.54Decreased
71Guanine nucleotide–binding protein (G protein), γ12GNG120.855.3E−04−0.50
72Discoidin, CUB and LCCL domain containing 2DCBLD20.851.2E−04−0.47Decreased
73Mastermind-like 2 (Drosophila)MAML20.851.6E−03−0.47
74Transforming growth factor, β receptor II (70/80 kDa)TGFBR20.856.0E−04−0.49
75Phosphoglucomutase 1PGM10.845.6E−03−0.45Increased
76Platelet-derived growth factor CPDGFC0.841.4E−04−0.59Decreased
77Integrin, α5 (fibronectin receptor, α-polypeptide)ITGA50.823.5E−03−0.40
78Chromosome 3 open reading frame 6C3orf60.823.2E−03−0.42
79IFN-induced protein with tetratricopeptide repeats 3IFIT30.828.1E−04−0.45
80Elongation factor, RNA polymerase II, 2ELL20.811.7E−03−0.44
81PALM2-AKAP2 proteinPALM2-AKAP20.811.2E−03−0.48Decreased
82CDC42 effector protein (Rho GTPase binding) 3CDC42EP30.811.1E−03−0.61Decreased
83ZyxinZYX0.81.0E−02−0.58
Resistant gene signature
84Solute carrier family 1 (glial high affinity glutamate transporter), member 2SLC1A2−1.771.8E−060.64
85Chromobox homologue 5 (HP1 α homologue, Drosophila)CBX5−1.531.5E−040.79
86239292_at−1.529.3E−050.58
87Degenerative spermatocyte homologue 2, lipid desaturase (Drosophila)DEGS2−1.453.7E−050.63
88Claudin 3CLDN3−1.441.1E−040.52
89KIAA0984 proteinKIAA0984−1.432.8E−040.42
90Phospholipase C, β4PLCB4−1.436.5E−050.55
91SH3-binding domain kinase 1SBK1−1.435.6E−050.68
92Islet cell autoantigen 1 (69 kDa)ICA1−1.44.6E−030.67
93Carbonic anhydrase XIICA12−1.332.5E−040.63
94Tumor protein D52TPD52−1.322.5E−050.51
95ATP-binding cassette, subfamily A (ABC1), member 3ABCA3−1.318.8E−060.76
96KIAA1324KIAA1324−1.311.1E−040.41
97DORA reverse strand protein 1DREV1−1.232.3E−050.62
98Ret finger protein 2RFP2−1.218.4E−030.60
99Solute carrier family 38, member 1SLC38A1−1.142.2E−030.48
100Cyclic AMP-responsive element binding protein 3–like 4CREB3L4−1.143.4E−030.42
101Chromosome 17 open reading frame 28C17orf28−1.147.6E−030.41
102Cisplatin resistance–associated overexpressed proteinCROP−1.114.2E−030.61
103Phospholipase C–like 3PLCL3−1.116.2E−040.42
104Abhydrolase domain containing 11ABHD11−1.099.2E−040.54
105230085_at−1.095.2E−050.57
106Arg/Abl-interacting protein ArgBP2ARGBP2−1.084.4E−030.54
107Solute carrier family 35 (CMP-sialic acid transporter), member A1SLC35A1−1.081.1E−040.64
108Solute carrier family 16 (monocarboxylic acid transporters), member 6SLC16A6−1.031.5E−030.51
109FLJ21963 proteinFLJ21963−1.027.4E−040.41
110ATP-binding cassette, subfamily G (WHITE), member 1ABCG1−1.029.7E−040.49
111Cytochrome b-561CYB561−1.023.1E−030.44
112Achaete-scute complex-like 2 (Drosophila)ASCL2−1.021.2E−040.50
113Insulin-like growth factor binding protein 2 (36 kDa)IGFBP2−1.019.9E−030.53
114Prolactin receptorPRLR−1.011.7E−030.44
115Glycerol-3-phosphate dehydrogenase 1-likeGPD1L−1.016.4E−040.41
116Junctophilin 1JPH1−17.3E−050.43
117Epidermal growth factor receptor pathway substrate 15–like 1EPS15L1−0.991.8E−030.67
118Programmed cell death 4 (neoplastic transformation inhibitor)PDCD4−0.987.2E−040.50Increased
119Microtubule-associated protein τMAPT−0.982.5E−040.65
120Chromosome 14 open reading frame 83C14orf83−0.974.2E−040.54
121Isochorismatase domain containing 1ISOC1−0.961.0E−030.46
122Aristaless-related homeoboxARX−0.953.7E−040.50
123Trichorhinophalangeal syndrome ITRPS1−0.951.8E−040.55
124239847_at−0.951.6E−030.43
125Vacuolar protein sorting 37C (yeast)VPS37C−0.955.1E−030.56
126LAG1 longevity assurance homologue 6 (S. cerevisiae)LASS6−0.941.2E−030.47
127Scavenger receptor class B, member 1SCARB1−0.946.6E−030.42
128Phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1PREX1−0.942.0E−030.46
129225996_at−0.942.0E−030.49
130Cholinergic receptor, muscarinic 1CHRM1−0.949.5E−050.52
131GREB1 proteinGREB1−0.931.5E−030.55
132Choline phosphotransferase 1CHPT1−0.923.4E−040.72
133Eukaryotic translation initiation factor 4E member 3EIF4E3−0.917.4E−030.58
134Ubiquitin-like 3UBL3−0.917.4E−030.52
135SpinsterSPIN1−0.95.2E−030.62
136Calmodulin 1 (phosphorylase kinase, δ)CALM1−0.93.9E−030.48
137Hypothetical LOC131076LOC131076−0.99.3E−030.54
138Phosphoinositide-3-kinase–related kinase SMG-1-likeDKFZp547E087−0.91.4E−030.52
139Myelin expression factor 2MYEF2−0.97.9E−030.59
140Solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15SLC25A15−0.896.1E−030.62
141Chromosome 6 open reading frame 108C6orf108−0.881.0E−030.67
142YME1-like 1 (S. cerevisiae)YME1L1−0.872.1E−030.50
143Williams-Beuren syndrome, critical region protein 20 copy BWBSCR20B−0.861.2E−030.59
144239065_at−0.859.4E−030.52
145Acyl-CoA synthetase long-chain family member 3ACSL3−0.848.2E−030.58
146230991_at−0.842.9E−030.43
147Trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in)TFF1−0.846.2E−040.45Increased
148Epithelial membrane protein 2EMP2−0.841.0E−020.47
149Chromosome 14 open reading frame 93C14orf93−0.835.1E−040.52
150START domain containing 10STARD10−0.838.9E−040.43Increased
151Ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)CLN3−0.831.6E−030.49
152Ras homologue gene family, member BRHOB−0.823.1E−030.42Increased
153Erythrocyte membrane protein band 4.1–like 5EPB41L5−0.817.8E−030.41
154Iroquois homeobox protein 5IRX5−0.81.0E−020.51
155Hypothetical protein LOC92482LOC92482−0.88.2E−030.48Increased
156CDC42 small effector 1CDC42SE1−0.81.0E−020.50
157Pleckstrin homology domain containing, family H (with MyTH4 domain) member 1PLEKHH1−0.797.5E−050.56
158EGF-like domain, multiple 5EGFL5−0.791.0E−020.52
159239319_at−0.781.5E−030.42
160Transducer of ERBB2, 1TOB1−0.783.9E−030.42Increased
161Crn, crooked neck-like 1 (Drosophila)CRNKL1−0.771.5E−030.44
  • NOTE: Sensitive and resistant gene signatures are listed separately and ranked by S2N score. Positive or negative signs correspond to gene g being more highly expressed in sensitive class or resistant class.

  • * For nonannotated genes, Affymetrix probe set ID are provided as the identification.

  • Correlation between the IC50 values and the expression level of each gene in cell lines was assessed by Pearson correlation coefficient r.

  • Eleven breast cell lines were treated with 0.1 μmol/L of dasatinib for 24 h. Pair-wise comparisons between cells treated with or without dasatinib were done, genes whose expressions were significantly increased or decreased in at least four cell lines were considered to be modulated by the drug treatment.