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 THY1 7070 ENSG00000154096 3.29 2.41E-04 9.76E-03 2994.5 2506.5 150.3 2389.9 150.0 195.0 TM4SF1 4071 ENSG00000169908 5.56 2.08E-08 3.16E-06 117.3 242.3 308.7 4.9 1.0 7.4 TMCO4 255104 ENSG00000162542 5.51 1.45E-04 6.41E-03 2.7 1.6 42.3 129.9 1.2 1.0 TMEM100 55273 ENSG00000166292 4.02 1.48E-03 4.03E-02 186.9 150.7 0.0 47.0 0.0 8.1 TMEM132D 121256 ENSG00000151952 -Inf 1.01E-04 4.75E-03 0.0 0.0 0.0 0.0 57.0 23.2 TMEM158 25907 2.67 1.85E-03 4.77E-02 535.5 466.7 154.3 1586.1 140.7 91.0 TMEM176B 28959 ENSG00000106565 6.03 2.07E-03 5.11E-02 20.3 93.6 0.0 5.5 0.0 1.0 TMEM200B 399474 ENSG00000187975 4.13 9.61E-04 2.87E-02 2.7 1.6 58.5 119.9 0.9 6.5 TMEM38A 79041 ENSG00000072954 3.09 1.80E-03 4.67E-02 205.9 608.9 70.7 5.1 33.3 20.2 TMEM71 137835 ENSG00000165071 -3.20 2.42E-03 5.74E-02 1.4 12.6 20.2 1.0 194.7 10.1 TMSB15A 11013 ENSG00000158164 -2.98 1.29E-03 3.62E-02 0.0 0.0 171.6 265.9 1121.9 1173.9 TMSL1 ENSG00000223551 -2.64 4.07E-03 8.65E-02 25.6 9.8 177.7 36.9 595.0 336.6 TNC 3371 ENSG00000041982 2.99 3.08E-04 1.19E-02 215.9 188.2 31.9 1597.5 59.8 91.8 TNFAIP2 7127 ENSG00000185215 6.89 5.19E-11 1.43E-08 0.0 0.0 28.1 513.3 0.0 3.0 TNFAIP3 7128 ENSG00000118503 2.86 3.34E-03 7.40E-02 16.2 17.2 83.3 177.3 0.0 25.7 TNFAIP6 7130 ENSG00000123610 4.95 8.74E-08 1.14E-05 621.2 458.0 6.8 288.5 0.0 15.8 TNFRSF14 8764 ENSG00000157873 4.01 2.55E-04 1.02E-02 12.7 7.9 67.4 260.7 12.9 1.0 TNFSF4 7292 ENSG00000117586 3.98 3.69E-06 3.06E-04 35.1 21.4 55.2 2851.5 58.6 64.6 TNNC2 7125 ENSG00000101470 -Inf 1.46E-04 6.41E-03 0.0 0.0 0.0 0.0 0.0 85.9 TNNI1 7135 ENSG00000159173 -Inf 2.55E-05 1.54E-03 0.0 0.0 0.0 0.0 0.0 116.0 TNNI2 7136 ENSG00000130598 -Inf 2.84E-05 1.67E-03 0.0 0.0 0.0 0.0 0.0 114.0 TOX 9760 ENSG00000198846 3.31 1.07E-03 3.15E-02 197.4 221.1 5.6 134.9 3.2 21.2 TPM1 7168 ENSG00000140416 -2.94 1.95E-03 4.92E-02 85.7 78.5 269.4 215.4 955.6 1911.5 TPMT 7172 ENSG00000137364 2.85 1.09E-03 3.17E-02 179.6 367.0 563.7 1733.5 198.9 47.9 TRAF1 7185 ENSG00000056558 3.92 2.00E-03 5.01E-02 17.9 36.3 19.5 145.7 6.8 2.0 TRAM1L1 133022 ENSG00000174599 -5.13 4.75E-05 2.50E-03 0.0 0.0 0.0 11.3 121.7 146.3 TRIB2 28951 ENSG00000071575 -2.05 1.95E-03 4.92E-02 434.9 352.2 34.9 55.8 919.1 307.4 TRIB3 57761 ENSG00000101255 3.42 5.71E-05 2.94E-03 83.9 109.6 4203.7 837.1 158.2 161.8 TRIM14 9830 ENSG00000106785 3.38 2.02E-03 5.05E-02 54.4 63.7 73.3 155.4 13.5 5.3 TRIM47 91107 ENSG00000132481 3.88 7.17E-06 5.33E-04 106.8 49.3 265.0 527.1 7.6 29.9 TRIM48 79097 ENSG00000150244 Inf 1.84E-04 7.84E-03 21.6 124.2 0.0 0.0 0.0 0.0 TRPM8 79054 ENSG00000144481 4.14 2.35E-05 1.45E-03 156.8 802.9 10.6 75.3 20.5 13.1 TSHZ3 57616 ENSG00000121297 4.45 2.11E-05 1.32E-03 136.6 142.5 38.5 184.1 0.0 11.1 TSLP 85480 ENSG00000145777 5.71 1.24E-04 5.63E-03 4.1 4.6 155.0 0.0 0.0 2.0 TSPAN13 27075 ENSG00000106537 2.62 1.25E-03 3.53E-02 126.1 234.5 127.9 748.4 28.1 91.9 TSPAN7 7102 ENSG00000156298 3.70 6.53E-05 3.32E-03 737.7 849.2 1.3 1.7 0.0 43.7 TSPAN9 10867 ENSG00000011105 2.72 2.51E-03 5.92E-02 78.4 90.4 99.0 4588.1 416.6 68.8 TSTD1 100131187 ENSG00000215845 4.79 1.38E-03 3.80E-02 0.0 0.0 127.5 0.0 0.0 2.7 TTF2 8458 ENSG00000116830 3.05 6.65E-04 2.17E-02 55.3 112.4 65.1 472.7 25.1 27.3 TTN 7273 ENSG00000155657 -Inf 2.68E-03 6.22E-02 0.0 0.0 0.0 0.0 0.0 45.5 TTYH1 57348 ENSG00000167614 -1.91 2.34E-03 5.61E-02 1960.4 834.0 0.0 21.2 1183.5 958.4 TUBA4A 7277 ENSG00000127824 4.85 2.91E-05 1.70E-03 54.0 47.9 185.7 29.1 0.0 6.1 TUBB4 10382 ENSG00000104833 4.59 1.43E-03 3.94E-02 150.5 113.6 32.7 0.0 0.0 3.6 TUSC3 7991 ENSG00000104723 -3.74 1.32E-04 5.89E-03 0.0 0.0 5.9 75.0 379.0 333.7 UGT8 7368 ENSG00000174607 4.64 4.89E-06 3.85E-04 155.7 274.5 169.2 38.9 3.8 8.6 UNC80 285175 ENSG00000144406 -1.98 4.34E-03 9.08E-02 113.5 162.2 0.0 38.7 322.5 207.8 VAX1 11023 ENSG00000148704 -Inf 2.74E-06 2.39E-04 0.0 0.0 0.0 0.0 32.7 121.6 VCAM1 7412 ENSG00000162692 4.34 1.49E-07 1.89E-05 0.0 0.0 46.0 2398.4 8.4 71.4 VIPR1 7433 ENSG00000114812 -4.43 4.74E-06 3.77E-04 6.5 3.1 66.7 6.8 1096.8 1.0 VIPR2 7434 ENSG00000106018 -Inf 2.65E-08 3.86E-06 0.0 0.0 0.0 0.0 216.4 15.9 VIT 5212 ENSG00000205221 6.07 1.83E-05 1.18E-03 14.9 12.4 0.0 193.0 0.0 2.1 VSNL1 7447 ENSG00000163032 3.76 1.35E-04 5.99E-03 0.0 1.6 16.2 332.9 0.0 16.7 248
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 WBSCR17 64409 ENSG00000185274 -Inf 3.18E-05 1.80E-03 0.0 0.0 0.0 0.0 17.6 90.9 XXbac-BPG116M5.1,C2,CFB 629,717 ENSG00000166278,ENSG00000243649,ENSG00000244255 3.95 4.11E-04 1.54E-02 5.4 4.0 98.3 132.4 0.0 10.6 XYLT1 64131 ENSG00000103489 4.78 1.10E-03 3.20E-02 174.3 164.9 0.0 0.8 0.0 4.0 ZEB1 6935 ENSG00000148516 -2.40 2.63E-03 6.14E-02 504.6 290.3 85.0 57.0 508.8 1006.3 ZIC2 7546 ENSG00000043355 -5.61 2.65E-05 1.59E-03 1.4 6.3 0.8 0.0 0.0 223.2 ZIC3 7547 ENSG00000156925 -Inf 2.12E-04 8.75E-03 0.0 0.0 0.0 0.0 0.0 79.8 ZIC4 84107 ENSG00000174963 -7.51 5.84E-04 1.95E-02 0.0 0.0 0.6 0.0 28.5 47.4 ZIC5 85416 ENSG00000139800 -7.19 6.13E-06 4.74E-04 0.0 1.6 0.6 0.0 0.0 211.7 ZNF281 23528 ENSG00000162702 5.45 4.39E-04 1.61E-02 60.6 51.6 81.7 0.0 0.0 2.0 ZNF423 23090 ENSG00000102935 -7.23 3.72E-07 4.29E-05 0.0 0.0 0.0 3.0 80.2 247.2 ZNF454 285676 ENSG00000178187 4.41 7.62E-05 3.75E-03 24.3 118.3 19.6 152.8 0.0 9.2 ZNF536 9745 ENSG00000198597 Inf 3.95E-05 2.18E-03 41.7 100.5 3.8 37.9 0.0 0.0 ZNF710 374655 ENSG00000140548 -4.55 3.99E-03 8.49E-02 4.1 2.1 5.3 0.0 33.8 68.7 ZNF714 148206 ENSG00000160352 Inf 2.07E-03 5.12E-02 86.5 59.1 18.8 0.0 0.0 0.0 ZNF747 65988 ENSG00000169955 Inf 4.62E-04 1.66E-02 12.2 9.5 14.6 71.1 0.0 0.0 249
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:
Page 199 and 200:
Page 201 and 202:
Page 203 and 204:
Page 205 and 206: 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 255: 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 307 and 308:
E. Exon Array Data Appendix Average
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?