STAT530lecture6DiffExprGene - Detecting differentially...

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1 Ping Ma STAT530 Detecting differentially expressed Detecting differentially expressed genes in comparative experiments genes in comparative experiments Ping Ma Ping Ma Ping Ma STAT530 Outline s Differential gene expression – Fold change – Parametric test: t and Welch-t test – Non-parametric test: permutation t and Wilcoxon s Multiple hypothesis testing – Family-wide error rate – FDR: Benjamini, SAM, and q-value s Gene ontology – hypergeometric distribution s Gene set enrichment analysis – KS test
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2 Ping Ma STAT530 probe set gene Normal m4 Normal m4 Normal m4 Normal m4 Normal m43 MM m282 MM m331aMM m332aMM m333aMM m334aMM m353aMM m408aMM m423a 31307_at pre-T/NK c 28.53 32.61 29.56 36.55 33.19 25.1 32.79 34.3 35.44 28.48 29.55 22.28 28.77 31308_at pre-T/NK c 69.14 53.69 52.78 62.07 58.74 67.88 85.82 83.54 85.91 60.93 62.82 47.17 77.07 31309_r_a Human bre 16.9 67.7 27.61 46.16 51.46 45.62 35.57 32.62 35.14 96.18 45.94 63.2 38.27 31310_at glycine rec 67.42 49.55 55.51 59.57 68.42 91.06 91.23 83.66 76.37 71.23 74.95 74.04 100.77 31311_at Homo sapi 78.73 62.91 60.84 72.98 72.9 79.39 85.52 82.57 69.69 63.72 64.29 62.85 67.58 31312_at potassium 66.65 59.46 55.47 61.75 69.92 75.28 85.53 97.91 69.92 74.77 71.83 58.17 72.15 31313_at mannosyl 115.33 95.51 84.48 94.99 109.04 105.05 118.68 106.76 142.88 103.72 106.19 98.58 104.13 31314_at bone morp 71.89 36.24 41.86 46.99 45.94 46.67 67.56 66.14 53.95 40.97 47.96 43.63 53.54 31315_at immunoglo 103.99 88.27 83.81 81.81 254.63 87.12 99.11 109.56 86.37 75.03 74.97 69.02 97.22 31316_at Human vac 16.79 10.08 9.53 16.48 11.98 12.8 16.7 18.76 11.25 12.09 18.89 10.81 19.49 31317_r_a Human un 316.75 269.61 254.92 352.61 342.4 327.12 366.39 346 308.43 279.81 312.4 318.06 334.27 31318_at Stem cel f 32.68 19.79 27.45 29.56 28.34 26.55 38.04 41.05 31.91 22.76 23.58 28.29 22.61 31319_at Cluster Inc 252.78 441.07 143.32 400.01 373.4 105.06 105.72 87.02 110.75 161.69 84.88 240.91 210.54 31320_at Cluster Inc 101.42 89.07 79.51 100.69 120.06 116.74 121.41 134.74 131.36 137.4 114.15 119.89 126.74 31321_at Cluster Inc 112.27 62.17 62.44 80.17 110.97 53.89 55.04 55.16 63.37 54.35 57.79 48.07 47.89 31322_at Cluster Inc 44.15 52.5 44.8 46.25 55.96 50.01 53.2 52.24 62.16 49.94 47.24 40.64 50.1 31323_r_a Glutamate 141.44 177.7 138.58 142.61 167.28 169.49 199.64 185.22 218.79 196.56 150.14 185.24 226.37 31324_at Cluster Inc 70.87 57.8 61.61 65.93 84.05 106.41 106.73 87.01 112.12 78.47 111 89.08 100.53 31325_at Cluster Inc 68.63 167.66 69.04 112.84 120.46 126.72 107.04 100 116.83 207.5 125.65 155.19 102.55 31326_at Cluster Inc 157.67 127.49 123.37 146.18 150.95 159.46 184.08 206.02 182.95 139.01 154.57 143.09 175.27 31327_at Cluster Inc 35.57 28.17 33.64 32.36 38.76 43.13 40.16 46.8 34.47 33.71 25.74 29.45 37.37 31328_at solute carr 61.61 48.23 50.76 58 57.58 57.91 69.91 72.34 70.29 54.98 59.74 45.55 63.02 31329_at Human pu 12.23 18.91 15.36 19.99 21.15 15.9 20.76 22.26 16.15 28.86 13.59 16.06 23.85 31330_at ribosomal 108.87 133.3
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STAT530lecture6DiffExprGene - Detecting differentially...

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