Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

More documents

Recommendations

Info

A.1 Differential Expression Appendix Gene symbol(s) Entrez gene ID(s) Ensembl 56 gene ID(s) Differential expression results Normalised tag counts log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660 GBP1 2633 ENSG00000117228 3.90 2.24E-04 9.22E-03 1.5 0.0 64.1 266.1 7.6 6.9 GBP2 2634 ENSG00000162645 4.06 6.94E-06 5.18E-04 0.0 4.7 468.3 654.3 41.3 4.0 GBP3 2635 ENSG00000117226 3.47 1.53E-04 6.69E-03 0.0 0.0 49.3 720.9 37.5 9.1 GBP4 115361 ENSG00000162654 Inf 3.54E-04 1.35E-02 7.5 0.0 15.3 82.2 0.0 0.0 GBP5 115362 ENSG00000154451 Inf 3.88E-09 6.87E-07 0.0 0.0 52.6 276.2 0.0 0.0 GCNT1 2650 ENSG00000187210 Inf 4.77E-03 9.74E-02 5.5 1.6 15.0 46.2 0.0 0.0 GDF15 9518 ENSG00000130513 4.37 3.15E-07 3.72E-05 288.9 1402.4 1358.2 108.3 22.8 69.9 GDPD2 54857 ENSG00000130055 -3.12 7.12E-04 2.27E-02 32.7 37.2 0.0 4.2 133.1 108.5 GEM 2669 ENSG00000164949 4.64 1.68E-06 1.57E-04 57.7 61.0 37.7 610.9 15.7 3.0 GFAP 2670 ENSG00000131095 5.34 1.43E-06 1.37E-04 468.5 336.4 0.0 94.7 0.0 7.2 GFPT2 9945 ENSG00000131459 2.25 4.84E-03 9.82E-02 24.3 15.6 247.6 243.2 0.0 70.6 GGH 8836 ENSG00000137563 2.45 4.70E-03 9.64E-02 899.6 886.6 7220.3 4880.1 475.4 1096.6 GJA1 2697 ENSG00000152661 -3.49 1.89E-04 8.00E-03 334.7 130.2 764.6 116.4 6363.9 1206.7 GJB2 2706 ENSG00000165474 2.80 1.20E-03 3.42E-02 1.4 0.0 18.4 448.1 0.0 44.0 GJC3 349149 ENSG00000176402 Inf 1.50E-03 4.05E-02 31.1 86.2 0.0 0.0 0.0 0.0 GLYATL2 219970 ENSG00000156689 -3.99 2.64E-03 6.15E-02 39.2 9.5 0.0 0.0 25.8 73.6 GMPR 2766 ENSG00000137198 3.72 2.86E-03 6.54E-02 108.1 140.1 33.5 35.5 4.5 6.3 GNG11 2791 ENSG00000127920 -2.33 3.49E-03 7.64E-02 393.2 316.9 345.3 1039.6 4802.2 908.6 GPC3 2719 ENSG00000147257 -5.79 1.24E-06 1.19E-04 0.0 0.0 35.1 0.0 11.6 1268.7 GPNMB 10457 ENSG00000136235 6.74 1.68E-11 5.42E-09 7688.5 16473.1 127.8 224.6 82.2 23.2 GPR158 57512 ENSG00000151025 -4.55 7.39E-08 9.89E-06 103.8 117.4 0.0 53.3 2311.0 354.9 GPR98 84059 ENSG00000164199 -3.99 2.40E-04 9.74E-03 30.5 20.0 4.4 0.0 76.9 183.8 GRB14 2888 ENSG00000115290 5.96 1.66E-03 4.39E-02 31.2 30.3 4.6 60.7 0.0 1.2 GRIA1 2890 ENSG00000155511 -4.42 3.62E-07 4.24E-05 33.1 68.7 2.7 73.4 1780.2 292.7 GRIA3 2892 ENSG00000125675 7.17 7.45E-05 3.71E-03 85.8 129.9 1.4 32.7 0.8 0.0 GRIK3 2899 ENSG00000163873 5.24 3.84E-07 4.35E-05 580.1 631.6 0.0 0.0 0.0 11.1 GRM3 2913 ENSG00000198822 -Inf 4.70E-08 6.47E-06 0.0 0.0 0.0 0.0 162.4 66.0 GYG2 8908 ENSG00000056998 -2.89 5.71E-04 1.93E-02 52.6 51.3 3.8 0.8 223.4 55.4 H1F0 3005 ENSG00000189060 3.59 9.61E-04 2.87E-02 93.7 46.8 89.0 103.7 0.0 13.5 HAND2 9464 ENSG00000164107 Inf 1.11E-03 3.22E-02 75.0 84.1 1.0 2.9 0.0 0.0 HAPLN1 1404 ENSG00000145681 6.40 4.55E-07 4.98E-05 521.8 383.7 0.0 0.0 0.0 3.0 HCP5 10866 ENSG00000206337 Inf 8.81E-09 1.49E-06 0.0 0.0 180.4 114.3 0.0 0.0 HEPACAM 220296 ENSG00000165478 Inf 3.91E-03 8.39E-02 82.3 65.6 0.0 3.0 0.0 0.0 HIF3A 64344 ENSG00000124440 -Inf 1.27E-03 3.56E-02 0.0 0.0 0.0 0.0 15.2 36.3 HLA-A 3105 ENSG00000206503 3.04 3.02E-04 1.18E-02 294.8 469.0 840.5 535.7 83.8 65.7 HLA-DMA 3108 ENSG00000204257 Inf 8.98E-07 9.08E-05 383.9 196.7 13.7 7.4 0.0 0.0 HLA-DPA1 3113 ENSG00000231389 5.73 5.76E-11 1.53E-08 1554.1 1033.9 49.5 243.3 4.6 12.4 HLA-DPB1 3115 ENSG00000223865 3.83 4.38E-04 1.61E-02 1007.2 359.8 0.6 12.3 2.4 15.1 HLA-DQA1 3117 ENSG00000196735 Inf 1.25E-03 3.53E-02 198.2 89.6 0.0 0.0 0.0 0.0 HLA-DQA2 3118 ENSG00000237541 6.56 5.45E-07 5.75E-05 0.0 0.0 8.1 280.8 0.0 2.4 HLA-DQB1 3119 ENSG00000179344 4.60 3.26E-05 1.84E-03 348.2 347.0 16.8 31.7 3.4 7.4 HLA-DRA 3122 ENSG00000204287 5.68 3.67E-09 6.58E-07 9744.0 5434.9 138.4 270.5 57.4 19.2 HLA-DRB3,HLA-DRB1,HLA- 3123,3125,3126 ENSG00000196126 Inf 2.04E-10 4.89E-08 1105.3 381.8 3.1 87.8 0.0 0.0 240 DRB4 HLA-DRB5 3127 ENSG00000198502 8.36 1.38E-13 6.04E-11 2885.9 995.1 0.0 0.0 0.0 2.0 HMGA2 8091 ENSG00000149948 -5.68 3.13E-07 3.72E-05 0.0 0.0 0.0 23.7 233.3 576.3 HOMER1 9456 ENSG00000152413 6.06 4.09E-05 2.24E-03 94.6 173.2 28.9 0.0 0.0 2.0 HOXA1 3198 ENSG00000105991 Inf 2.21E-03 5.39E-02 13.5 10.9 12.5 48.3 0.0 0.0 HOXA10 3206 ENSG00000153807 Inf 8.63E-14 4.42E-11 479.4 631.7 19.5 273.5 0.0 0.0 HOXA4 3201 ENSG00000197576 Inf 4.31E-11 1.26E-08 63.1 100.0 2.5 382.0 0.0 0.0 HOXA5 3202 ENSG00000106004 Inf 3.20E-03 7.17E-02 22.7 33.6 2.5 33.1 0.0 0.0 HOXA7 3204 ENSG00000122592 Inf 5.79E-04 1.94E-02 51.7 102.1 0.7 0.0 0.0 0.0
A.1 Differential Expression Appendix Gene symbol(s) Entrez gene ID(s) Ensembl 56 gene ID(s) Differential expression results Normalised tag counts log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660 HOXB6 3216 ENSG00000108511 Inf 1.08E-03 3.16E-02 0.0 0.0 23.8 59.8 0.0 0.0 HOXB7 3217 ENSG00000120087 Inf 2.51E-14 1.43E-11 0.0 0.0 795.3 109.6 0.0 0.0 HOXB9 3219 ENSG00000170689 Inf 2.50E-10 5.72E-08 0.0 0.0 338.7 55.6 0.0 0.0 HOXC10 3226 ENSG00000180818 Inf 1.74E-06 1.62E-04 90.5 160.7 47.1 0.0 0.0 0.0 HOXC13 3229 ENSG00000123364 Inf 2.48E-03 5.86E-02 3.5 76.4 0.5 0.0 0.0 0.0 HOXD10 3236 ENSG00000128710 Inf 7.25E-14 3.85E-11 77.0 145.9 115.3 578.2 0.0 0.0 HOXD13 3239 ENSG00000128714 Inf 2.33E-05 1.44E-03 27.2 45.4 0.0 93.3 0.0 0.0 HOXD3 3232 ENSG00000128652 Inf 4.05E-03 8.61E-02 49.4 40.5 1.5 25.7 0.0 0.0 HOXD9 3235 ENSG00000128709 Inf 7.80E-04 2.42E-02 49.7 61.6 23.2 7.4 0.0 0.0 HPRT1 3251 ENSG00000165704 2.62 6.73E-04 2.18E-02 28.4 82.7 614.7 246.9 4.3 96.9 HPSE 10855 ENSG00000173083 6.28 4.17E-04 1.56E-02 10.8 16.0 18.2 84.8 0.0 1.0 HRCT1 646962 ENSG00000196196 6.40 1.67E-03 4.42E-02 0.0 0.0 89.8 6.6 0.8 0.0 HTATIP2 10553 ENSG00000109854 7.51 1.09E-14 7.73E-12 38.0 50.0 3.8 1331.9 0.0 4.7 ICAM1 3383 ENSG00000090339 2.75 7.47E-04 2.35E-02 138.3 272.9 100.5 848.2 28.1 92.5 ID4 3400 ENSG00000172201 -2.33 4.89E-04 1.73E-02 1342.6 1447.2 17.6 161.5 4504.8 958.5 IFI27 3429 ENSG00000165949 3.86 2.55E-05 1.54E-03 11.8 7.4 446.9 38.2 2.3 20.5 IFI30 10437 ENSG00000216490 4.27 2.84E-06 2.47E-04 25.7 40.6 470.2 277.2 16.3 11.1 IFI6 2537 ENSG00000126709 3.36 2.69E-05 1.60E-03 110.0 57.7 2294.7 801.8 29.0 175.0 IFITM2 10581 ENSG00000185201 -4.89 3.84E-05 2.13E-03 0.0 0.0 31.2 8.3 0.0 775.8 IFITM8P ENSG00000215096 -Inf 2.27E-03 5.50E-02 0.0 0.0 0.0 0.0 0.6 46.3 IGF2,INS,INS- 3481,3630,723961 ENSG00000129965,ENSG00000167244,ENSG00000240801 -7.34 3.37E-08 4.77E-06 0.0 0.0 0.6 4.5 2.8 505.9 241 IGF2,AC132217.2 IGFBP5 3488 ENSG00000115461 -2.23 4.78E-03 9.74E-02 840.8 936.7 30.1 1081.5 3234.4 3148.3 IGLON5 402665 ENSG00000142549 5.38 1.58E-07 1.98E-05 750.3 630.9 0.0 0.0 0.0 10.1 IGSF11 152404 ENSG00000144847 3.49 7.56E-04 2.37E-02 453.7 549.5 0.0 0.0 14.7 18.3 IGSF3 3321 ENSG00000143061 3.78 5.11E-04 1.77E-02 301.4 260.7 41.9 45.7 6.9 10.0 IKBKE 9641 ENSG00000143466 -4.25 2.18E-03 5.35E-02 7.4 2.3 2.1 3.3 82.9 22.2 IL13RA2 3598 ENSG00000123496 5.66 2.22E-11 7.02E-09 0.0 0.0 451.0 628.7 0.0 14.3 IL17RD 54756 ENSG00000144730 -4.38 1.14E-05 8.03E-04 25.5 17.5 9.8 15.3 364.6 230.4 IL1B 3553 ENSG00000125538 Inf 1.93E-08 2.96E-06 0.0 0.0 115.5 175.1 0.0 0.0 IL1R1 3554 ENSG00000115594 2.49 1.56E-03 4.18E-02 25.7 15.0 67.6 977.0 19.4 104.7 IL1RAPL1 11141 ENSG00000169306 5.30 1.20E-03 3.42E-02 81.1 75.0 1.4 43.5 0.0 2.3 IL33 90865 ENSG00000137033 -Inf 1.60E-03 4.26E-02 0.0 0.0 0.0 0.0 0.0 51.2 IL4I1 259307 ENSG00000104951 6.01 1.36E-03 3.77E-02 2.7 2.1 12.6 84.2 0.0 1.0 IL6 3569 ENSG00000136244 Inf 7.89E-07 8.09E-05 44.6 25.3 110.4 64.6 0.0 0.0 IL8 3576 ENSG00000169429 7.68 4.39E-08 6.10E-06 0.0 0.0 26.4 286.9 0.0 1.5 INHBA 3624 ENSG00000122641 7.38 1.07E-06 1.05E-04 86.5 172.1 66.0 16.5 0.0 1.0 INHBB 3625 ENSG00000163083 5.89 2.05E-06 1.87E-04 240.6 361.5 0.0 0.0 0.0 4.1 INPP5D 3635 ENSG00000168918 -3.50 4.59E-03 9.47E-02 6.8 10.9 3.8 0.0 61.6 49.5 INSIG1 3638 ENSG00000186480 2.68 1.89E-03 4.84E-02 780.8 1475.9 1531.6 3387.9 282.2 383.3 IRAK1 3654 ENSG00000184216 2.95 4.63E-04 1.66E-02 292.6 279.4 764.0 375.0 75.1 46.1 IRX1 79192 ENSG00000170549 -3.75 4.11E-03 8.72E-02 30.5 11.4 0.0 0.0 5.1 92.7 IRX2 153572 ENSG00000170561 -4.65 1.01E-05 7.21E-04 0.0 0.0 0.0 28.9 370.0 111.1 ISYNA1 51477 ENSG00000105655 -2.54 3.24E-03 7.22E-02 308.0 123.3 127.2 149.7 668.8 883.1 ITGA4 3676 ENSG00000115232 2.99 9.76E-04 2.91E-02 70.2 63.0 11.9 594.6 35.7 20.2 ITGBL1 9358 ENSG00000198542 Inf 1.12E-03 3.24E-02 0.0 0.0 33.4 48.5 0.0 0.0 ITIH5 80760 ENSG00000123243 5.87 3.70E-10 8.21E-08 1336.6 1302.0 2.8 1.4 3.6 10.7 ITM2A 9452 ENSG00000078596 -Inf 4.47E-05 2.40E-03 0.0 0.0 0.0 0.0 0.0 105.8 JAM2 58494 ENSG00000154721 -2.11 3.94E-03 8.44E-02 196.8 310.6 12.5 199.1 780.0 726.7 JPH1 56704 ENSG00000104369 6.70 5.47E-05 2.84E-03 36.3 77.3 31.3 50.7 0.0 1.0 KALRN 8997 ENSG00000160145 -5.25 2.09E-06 1.88E-04 0.0 6.3 2.5 7.1 302.9 106.2 KANK1 23189 ENSG00000107104 2.97 8.79E-04 2.67E-02 374.9 583.2 79.6 135.3 14.5 53.9
Page 1 and 2:
Transcriptional Characterization of
Page 3 and 4:
This dissertation is my own work an
Page 5 and 6:
Acknowledgements I would like to th
Page 7 and 8:
5.9 External Dataset Expression Cor
Page 9 and 10:
Introduction 1
Page 11 and 12:
1.1 Glial Cells in the Central Nerv
Page 13 and 14:
1.2 Glioblastoma Multiforme Introdu
Page 15 and 16:
Page 17 and 18:
Page 19 and 20:
1.3 Primary and Secondary Glioblast
Page 21 and 22:
Page 23 and 24:
Page 25 and 26:
Page 27 and 28:
Page 29 and 30:
1.4 Pathways Involved in Glioblasto
Page 31 and 32:
Page 33 and 34:
Page 35 and 36:
Page 37 and 38:
Page 39 and 40:
1.5 Pathway Crosstalk Introduction
Page 41 and 42:
Chapter 2 Neurogenesis Contents 2.1
Page 43 and 44:
2.1 Radial Glia Introduction VZ adj
Page 45 and 46:
2.2 Neural Stem Cells Introduction
Page 47 and 48:
Page 49 and 50:
Page 51 and 52:
Page 53 and 54:
Page 55 and 56:
Page 57 and 58:
Page 59 and 60:
Page 61 and 62:
Page 63 and 64:
Page 65 and 66:
Chapter 3 Brain Cancer Stem Cells C
Page 67 and 68:
3.1 The Cancer Stem Cell Hypothesis
Page 69 and 70:
3.1 The Cancer Stem Cell Hypothesis
Page 71 and 72:
3.2 Brain Cancer Stem Cells Introdu
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Page 79 and 80:
Page 81 and 82:
3.3 Glioma Culture Systems Introduc
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
Page 89 and 90:
Page 91 and 92:
Page 93 and 94:
Chapter 4 The Non-Coding RNA World
Page 95 and 96:
4.1 MicroRNA regulation Introductio
Page 97 and 98:
4.1 MicroRNA regulation Introductio
Page 99 and 100:
4.2 Target Prediction and Validatio
Page 101 and 102:
Methods 93
Page 103 and 104:
5.1 Tag-sequencing Data Processing
Page 105 and 106:
5.1 Tag-sequencing Data Processing
Page 107 and 108:
5.2 Array Comparative Genomic Hybri
Page 109 and 110:
5.4 Quantitative Real Time-PCR Vali
Page 111 and 112:
Page 113 and 114:
Page 115 and 116:
5.5 Literature Mining Methods Figur
Page 117 and 118:
5.5 Literature Mining Methods How m
Page 119 and 120:
5.6 Differential Isoform Expression
Page 121 and 122:
5.9 External Dataset Expression Cor
Page 123 and 124:
5.10 Glioblastoma Pathway Construct
Page 125 and 126:
5.11 MicroRNA Target Prediction Ana
Page 127 and 128:
Results 119
Page 129 and 130:
6.2 Tag mapping Results Table 6.1:
Page 131 and 132:
6.2 Tag mapping Results 123 Figure
Page 133 and 134:
6.3 Copy Number Aberrations Results
Page 135 and 136:
6.3 Copy Number Aberrations Results
Page 137 and 138:
6.4 Core Differentially Expressed G
Page 139 and 140:
Page 141 and 142:
Page 143 and 144:
Page 145 and 146:
6.5 Large-scale qRT-PCR Validation
Page 147 and 148:
Page 149 and 150:
Page 151 and 152:
6.6 Literature Mining for Different
Page 153 and 154:
6.7 Isoform Differential Expression
Page 155 and 156:
Page 157 and 158:
Page 159 and 160:
Page 161 and 162:
Page 163 and 164:
Page 165 and 166:
6.8 Long ncRNA Differential Express
Page 167 and 168:
6.8 Long ncRNA Differential Express
Page 169 and 170:
Chapter 7 Dataset Correlation Analy
Page 171 and 172:
7.1 Enrichment Analysis Results Tab
Page 173 and 174:
7.1 Enrichment Analysis Results Fig
Page 175 and 176:
7.1 Enrichment Analysis Results Tab
Page 177 and 178:
7.2 Glioblastoma Expression Signatu
Page 179 and 180:
7.3 Tumour Expression Correlation R
Page 181 and 182:
Page 183 and 184:
Page 185 and 186:
Page 187 and 188:
Page 189 and 190:
Page 191 and 192:
7.4 Survival Analysis Results Table
Page 193 and 194:
7.4 Survival Analysis Results 867 g
Page 195 and 196:
7.5 Glioblastoma Pathway Analysis R
Page 197 and 198: 7.5 Glioblastoma Pathway Analysis R
Page 211 and 212: 8.1 Principles Results say, this is
Page 213 and 214: 8.3 Databases Results Figure 8.1: O
Page 215 and 216: 8.3 Databases Results Figure 8.3: W
Page 217 and 218: 8.4 Filters Results Bayesian method
Page 219 and 220: 8.5 Target Prediction Ensemble Anal
Page 229 and 230: 9.1. Digital Profiling of GNS Cell
Page 239 and 240: 9.2. MicroRNA Target Prediction Ana
Page 241 and 242: 9.3. Concluding Remarks Appendix pr
Page 243 and 244: A.1 Differential Expression Appendi
Page 247: A.1 Differential Expression Appendi
Page 259 and 260: A.2 Classified Differential Express
Page 265 and 266: A.3 Quantitative RT-PCR Appendix Ta
Page 267 and 268: A.3 Quantitative RT-PCR Appendix We
Page 269 and 270: A.3 Quantitative RT-PCR Appendix Ta
Page 271 and 272: A.3 Quantitative RT-PCR Appendix We
Page 273 and 274: A.4 Tag-seq vs qRT-PCR Correlation
Page 275 and 276: Appendix "BEX5", "DIAPH2", "GBP3",
Page 277 and 278: End Select End If End Sub Appendix
Page 279 and 280: If NameStr.ToLower().Equals("query"
Page 281 and 282: Appendix C Long ncRNAs We detected
Page 283 and 284: C. Long ncRNAs Appendix Tag Accessi
Page 285 and 286: D.1 Pathway Interactions Appendix F
Page 291 and 292: D.2 Pathway Images Appendix Figure
Page 293 and 294: D.2 Pathway Images Appendix Figure
Page 295 and 296: E. Exon Array Data Appendix Average
Page 297 and 298: E. Exon Array Data Appendix Average
Page 299 and 300:
E. Exon Array Data Appendix Average
Page 301 and 302:
Page 303 and 304:
Page 305 and 306:
Page 307 and 308:
Page 309 and 310:
F. MicroRNA Array Data Appendix Tab
Page 311 and 312:
F. MicroRNA Array Data Appendix GNS
Page 313 and 314:
F. MicroRNA Array Data Appendix GNS
Page 315 and 316:
Ln Natural logarithm LOH Loss of He
Page 317 and 318:
3.3 Schematisation of cell cycle ph
Page 319 and 320:
8.3 Workflows at the core of the pr
Page 321 and 322:
7.1 Selected Gene Ontology terms an
Page 323 and 324:
Bibliography [1] Cell signaling tec
Page 325 and 326:
[38] G. Bain, D. Kitchens, M. Yao,
Page 327 and 328:
[78] S. Bustin, V. Benes, J. Garson
Page 329 and 330:
[112] M. Czystowska, J. Han, M. Szc
Page 331 and 332:
[153] T. Fujiwara, M. Bandi, M. Nit
Page 333 and 334:
[192] M. Hernandez, M. Nieto, and M
Page 335 and 336:
[231] T.-M. Kim, W. Huang, R. Park,
Page 337 and 338:
[268] H. Lemjabbar-Alaoui, A. van Z
Page 339 and 340:
[305] K. MAEDA, S. MATSUHASHI, K. T
Page 341 and 342:
[342] H. Moon, M. Ahn, J. Park, K.
Page 343 and 344:
[379] D. Park and J. Rich. Biology
Page 345 and 346:
[417] P. Rakic. Guidance of neurons
Page 347 and 348:
[456] T. Shima, N. Okumura, T. Taka
Page 349 and 350:
[490] P. A. C. t’Hoen, Y. Ariyure
Page 351 and 352:
[523] T. Watanabe, A. Takeda, T. Ts
show all

Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?