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2 Number of Genes That Passed Filtering Criteria Description of the problem: Number of classes: 2 Number of genes that passed filtering criteria: 25338 Column of the Experiment Descriptors sheet that defines class variable: Sensitivity Number of arrays in each class: 24 in class label Resistant , 32 in class label Sensitive Feature selection criteria: Genes with univariate mis-classfication rate below 0.2 were used for class prediction. Cross-validation method: Leave-one-out cross-validation method was used to compute mis-classification rate. Performance of classifiers during cross-validation. Diagonal Mean Linear Number of Array id Class label Discriminant genes in Analysis classifier Correct? 1 CALU1 Resistant 129 YES 2 CAMA1 Resistant 155 YES 3 HCC1143 Resistant 145 YES 4 HCC1419 Resistant 148 YES 5 HCC2935 Resistant 136 YES 6 NCIH2405 Resistant 148 YES 7 SKBR3 Resistant 142 YES 8 ZR751 Resistant 133 YES 9 HCC1954 Resistant 147 YES 10 NCIH1651 Resistant 139 YES 11 NCIH226 Resistant 142 YES 12 T47D Resistant 139 YES 13 NCIH747 Resistant 146 YES 14 NCIH345 Resistant 216 NO 15 DLD1 Resistant 179 NO 16 NCIH1666 Resistant 154 YES 17 BT20 Resistant 140 YES 18 NCIH196 Resistant 168 NO 19 NCIH1437 Resistant 159 YES 20 MDAMB157 Resistant 158 YES 21 LS123 Resistant 155 YES 22 NCIH2347 Resistant 133 YES 23 MDAMB361 Resistant 137 YES 24 BT474 Resistant 155 YES 25 MDAMB468 Sensitive 182 NO 26 MCF10 Sensitive 169 NO 27 NCIH209 Sensitive 128 YES 28 RKO Sensitive 141 YES 29 HCC70 Sensitive 182 NO 30 LS513 Sensitive 136 YES 31 NCIH1963 Sensitive 122 YES 32 HCC1187 Sensitive 145 YES 33 T84 Sensitive 144 YES 34 COLO205 Sensitive 141 YES 35 LS1034 Sensitive 136 YES 36 NCIH69 Sensitive 130 YES 37 NCIH187 Sensitive 131 YES 38 HCT116 Sensitive 146 YES 39 NCIH1184 Sensitive 160 NO 40 NCIH508 Sensitive 124 YES 41 SNUC1 Sensitive 134 YES 42 HCC38 Sensitive 189 NO 43 NCIN592 Sensitive 121 YES 44 SW403 Sensitive 131 YES 45 NCIH378 Sensitive 124 YES 46 NCIH446 Sensitive 131 YES 47 LS174T Sensitive 128 YES 48 NCIH82 Sensitive 130 YES 49 NCIH2107 Sensitive 125 YES 50 SKCO1 Sensitive 133 YES 51 NCIN417 Sensitive 122 YES 52 NCIH889 Sensitive 123 YES 53 SW48 Sensitive 142 YES 54 MX1 Sensitive 139 YES 55 NCIH524 Sensitive 121 YES 56 NCIH716 Sensitive 140 YES Mean percent of correct 86 classification: Performance of classifiers during cross-valudation: Let, for some class A, n11 = number of class A samples predicted as A n12 = number of class A samples predicted as non-A n21 = number of non-A samples predicted as A n22 = number of non-A samples predicted as non-A Then the following parameters can characterize performance of classifiers: Sensitivity = n11/(n11+n12) Specificity = n22/(n21+n22) Positive Predictive Value (PPV) = n11/(n11+n21) Negative Predictive Value (NPV) = n22/(n12+n22) Sensitivity is the probability for a class A sample to be correctly predicted as class A, Specificity is the probability for a non class A sample to be correctly predicted as non-A, PPV is the probability that a sample predicted as class A actually belongs to class A, NPV is the probability that a sample predicted as non class A actually does not belong to class A. For each classification method and each class, these parameters are listed in the tables below Performance of the Diagonal Linear Discriminant Analysis Classifier: Sensitivity Specificity PPV NPV Class Resistant 0.875 0.844 0.808 0.9 Sensitive 0.844 0.875 0.9 0.808 Composition of classifier: Table - Sorted by t -value: Class 1: Resistant; Class 2: Sensitive. Geom mean of Geom mean of Parametric % CV Fold- Anno- t-value intensities in intensities in Probe set Gene symbol Description p-value support change tations class 1 class 2 1 < 1e-07 -7.953 100 161.5 2792.81 0.058 223092_at Info ANKH ankylosis, progressive homolog (mouse) 2 < 1e-07 -7.878 100 22.43 247.23 0.091 223093_at Info ANKH ankylosis, progressive homolog (mouse) 3 < 1e-07 -6.851 100 48.39 348.8 0.14 229930_at Info LOC100134361 similar to hCG1811002 4 < 1e-07 -6.163 100 38.7 224.56 0.17 223094_s_at Info ANKH ankylosis, progressive homolog (mouse) jumonji C domain containing histone demethylase 1 5 2e-07 -5.906 100 74.82 377.74 0.2 221778_at Info JHDM1D homolog D (S. cerevisiae) 6 4e-07 -5.76 100 37.33 676.91 0.055 228956_at Info UGT8 UDP glycosyltransferase 8 7 4e-07 -5.759 100 488.6 878.41 0.56 204387_x_at Info MRP63 mitochondrial ribosomal protein 63 8 6e-07 -5.677 100 252.62 714.42 0.35 214106_s_at Info GMDS GDP-mannose 4,6-dehydratase 9 1.1e-06 -5.502 100 487.47 1704.71 0.29 213610_s_at Info KLHL23 kelch-like 23 (Drosophila) 10 1.2e-06 -5.464 100 542.6 1036.5 0.52 218515_at Info C21orf66 chromosome 21 open reading frame 66 11 1.2e-06 -5.458 100 1752.76 3419.04 0.51 212175_s_at Info AK2 adenylate kinase 2 12 1.2e-06 -5.457 100 18.52 61.42 0.3 227563_at Info FAM27E3 family with sequence similarity 27, member E3 erythrocyte membrane protein band 4.1 (elliptocytosis 1, 13 1.3e-06 -5.449 100 472.09 1554.45 0.3 225051_at Info EPB41 RH-linked) 14 2e-06 -5.326 100 18995.02 27920.99 0.68 200772_x_at Info PTMA prothymosin, alpha 15 3.7e-06 -5.153 100 80.36 436.17 0.18 209815_at Info PTCH1 patched homolog 1 (Drosophila) 16 3.9e-06 -5.139 100 347.79 832.47 0.42 224450_s_at Info RIOK1 RIO kinase 1 (yeast) 17 4.2e-06 -5.119 100 8.95 39.57 0.23 220076_at Info ANKH ankylosis, progressive homolog (mouse) 18 4.5e-06 -5.099 100 368.15 922.28 0.4 235587_at Info LOC202781 hypothetical LOC202781 19 6.3e-06 -5.004 100 139.22 614.97 0.23 219976_at Info HOOK1 hook homolog 1 (Drosophila) ArfGAP with GTPase domain, ankyrin repeat and PH 20 6.8e-06 -4.984 100 359.43 725.65 0.5 225789_at Info AGAP3 domain 3 21 6.9e-06 -4.98 100 32.58 183.03 0.18 230403_at Info NA NA solute carrier family 7 (cationic amino acid transporter, 22 8.2e-06 -4.93 100 2676.72 5311.85 0.5 212295_s_at Info SLC7A1 y+ system), member 1 23 9.4e-06 -4.892 100 367.41 980.59 0.37 204875_s_at Info GMDS GDP-mannose 4,6-dehydratase 24 1e-05 -4.875 100 41.38 228.43 0.18 213713_s_at Info GLB1L2 galactosidase, beta 1-like 2 DNA fragmentation factor, 40kDa, beta polypeptide 25 1.06e-05 -4.857 100 18.47 59.53 0.31 206752_s_at Info DFFB (caspase-activated DNase) 26 1.2e-05 -4.823 100 22.29 468.69 0.048 214651_s_at Info HOXA9 homeobox A9 1-acylglycerol-3-phosphate O-acyltransferase 5 27 1.64e-05 -4.732 100 1123.47 2422.34 0.46 218096_at Info AGPAT5 (lysophosphatidic acid acyltransferase, epsilon) 28 2.24e-05 -4.643 100 158.09 558.22 0.28 218829_s_at Info CHD7 chromodomain helicase DNA binding protein 7 29 2.82e-05 -4.576 100 7.75 23.82 0.33 238898_at Info NA NA 30 2.86e-05 -4.572 100 1566.5 3357.39 0.47 224879_at Info C9orf123 chromosome 9 open reading frame 123 31 3.15e-05 -4.543 100 1174.57 1990.27 0.59 224890_s_at Info C7orf59 chromosome 7 open reading frame 59 myeloid/lymphoid or mixed-lineage leukemia (trithorax 32 3.5e-05 -4.512 100 6.97 22.1 0.32 244110_at Info MLL homolog, Drosophila) 33 4.22e-05 -4.458 100 1000.61 1659.53 0.6 218512_at Info WDR12 WD repeat domain 12 34 4.35e-05 -4.449 100 465.32 840.99 0.55 212931_at Info TCF20 transcription factor 20 (AR1) 35 5.23e-05 -4.395 100 1928.59 3839.96 0.5 202279_at Info C14orf2 chromosome 14 open reading frame 2 36 5.36e-05 -4.387 100 2848.2 8916.04 0.32 200644_at Info MARCKSL1 MARCKS-like 1 37 5.53e-05 -4.378 100 28.44 63.65 0.45 225595_at Info CREBZF CREB/ATF bZIP transcription factor 38 5.91e-05 -4.359 100 74.89 235.06 0.32 210006_at Info ABHD14A abhydrolase domain containing 14A 39 6.33e-05 -4.338 100 702.65 1598.15 0.44 218491_s_at Info THYN1 thymocyte nuclear protein 1 40 7.56e-05 -4.286 100 350.21 1054.39 0.33 225390_s_at Info KLF13 Kruppel-like factor 13 SWI/SNF related, matrix associated, actin dependent 41 7.74e-05 -4.278 100 1378.37 2195.94 0.63 201074_at Info SMARCC1 regulator of chromatin, subfamily c, member 1 O-linked N-acetylglucosamine (GlcNAc) transferase 42 7.96e-05 -4.27 100 1658.22 2800.08 0.59 209240_at Info OGT (UDP-N-acetylglucosamine:polypeptide-N- acetylglucosaminyl transferase) 43 8.34e-05 -4.256 100 26.85 92.59 0.29 224327_s_at Info DGAT2 diacylglycerol O-acyltransferase homolog 2 (mouse) 44 8.73e-05 -4.242 100 491.14 788.42 0.62 1553987_at Info C12orf47 chromosome 12 open reading frame 47 45 8.82e-05 -4.239 100 23.15 63.24 0.37 239835_at Info KBTBD8 kelch repeat and BTB (POZ) domain containing 8 46 9.61e-05 -4.214 100 14.45 104.26 0.14 229376_at Info PROX1 prospero homeobox 1 47 0.0001027 -4.194 100 376.32 725.8 0.52 225478_at Info MFHAS1 malignant fibrous histiocytoma amplified sequence 1 RCD1 required for cell differentiation1 homolog (S.
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