Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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E. Exon Array Data Appendix Average expression across samples Fold-change p-value FDR Ensembl Gene ID Symbol 8.68 0.866 0.000 0.000010 ENSG00000073578 SDHA 6.03 3.092 0.000 0.000010 ENSG00000089127 OAS1 3.57 1.6 0.000 0.000010 ENSG00000092607 TBX15 4.82 1.835 0.000 0.000010 ENSG00000102445 KIAA0226L 4.8 1.261 0.000 0.000010 ENSG00000103723 AP3B2 7.97 0.683 0.000 0.000010 ENSG00000106263 EIF3B 7.77 1.071 0.000 0.000010 ENSG00000121083 DYNLL2 6.83 1.603 0.000 0.000010 ENSG00000123146 CD97 6.29 0.672 0.000 0.000010 ENSG00000125746 EML2 7.19 0.883 0.000 0.000010 ENSG00000130305 NSUN5 7.03 2.957 0.000 0.000010 ENSG00000146072 TNFRSF21 4.7 1.327 0.000 0.000010 ENSG00000151117 TMEM86A 4.81 1.072 0.000 0.000010 ENSG00000153790 C7orf31 5.74 2.749 0.000 0.000010 ENSG00000166741 NNMT 5.11 1.937 0.000 0.000010 ENSG00000186088 PION 4.71 1.77 0.000 0.000010 ENSG00000187098 MITF 3.72 1.906 0.000 0.000010 ENSG00000204397 CARD16 7.31 1.009 0.000 0.000010 ENSG00000232098 AC012313.1 6.94 1.111 0.000 0.000020 ENSG00000072071 LPHN1 5.36 2.843 0.000 0.000020 ENSG00000089041 P2RX7 7.79 0.858 0.000 0.000020 ENSG00000089057 SLC23A2 5.99 1.358 0.000 0.000020 ENSG00000096433 ITPR3 8.6 0.812 0.000 0.000020 ENSG00000101474 APMAP 6.01 0.937 0.000 0.000020 ENSG00000103241 FOXF1 7.4 0.773 0.000 0.000020 ENSG00000105518 TMEM205 4.7 3.12 0.000 0.000020 ENSG00000106688 SLC1A1 4.11 1.188 0.000 0.000020 ENSG00000107864 CPEB3 6.82 1.511 0.000 0.000020 ENSG00000110841 PPFIBP1 6.66 1.511 0.000 0.000020 ENSG00000117280 RAB7L1 8.48 1.567 0.000 0.000020 ENSG00000125148 MT2A 5.93 2.858 0.000 0.000020 ENSG00000125820 NKX2-2 6.31 2.012 0.000 0.000020 ENSG00000134202 GSTM3 3.83 1.725 0.000 0.000020 ENSG00000134716 CYP2J2 4.06 1.958 0.000 0.000020 ENSG00000136237 RAPGEF5 7.69 2.759 0.000 0.000020 ENSG00000136842 TMOD1 6.32 0.922 0.000 0.000020 ENSG00000141026 MED9 6.37 1.279 0.000 0.000020 ENSG00000147889 CDKN2A 5.91 1.256 0.000 0.000020 ENSG00000158856 EPB49 7.98 1.855 0.000 0.000020 ENSG00000162873 KLHDC8A 6.97 0.685 0.000 0.000020 ENSG00000167106 FAM102A 6.31 3.628 0.000 0.000020 ENSG00000170689 HOXB9 5.8 1.171 0.000 0.000020 ENSG00000172183 ISG20 4.23 1.273 0.000 0.000020 ENSG00000172345 STARD5 7.02 1.316 0.000 0.000020 ENSG00000176490 DIRAS1 6.55 0.867 0.000 0.000020 ENSG00000177556 ATOX1 5.87 2.507 0.000 0.000020 ENSG00000196361 ELAVL3 5.22 0.873 0.000 0.000020 ENSG00000196476 C20orf96 5.9 1.137 0.000 0.000020 ENSG00000196683 TOMM7 8.22 1.421 0.000 0.000020 ENSG00000205362 MT1A 4.9 1.465 0.000 0.000030 ENSG00000018869 ZNF582 6.66 0.818 0.000 0.000030 ENSG00000101181 GTPBP5 5.69 1.972 0.000 0.000030 ENSG00000113296 THBS4 5.74 1.581 0.000 0.000030 ENSG00000119922 IFIT2 6.83 0.596 0.000 0.000030 ENSG00000130813 C19orf66 6.99 1.327 0.000 0.000030 ENSG00000145216 FIP1L1 5.26 1.11 0.000 0.000030 ENSG00000149927 DOC2A 4.84 1.528 0.000 0.000030 ENSG00000151090 THRB 7.77 1.094 0.000 0.000030 ENSG00000157259 GATAD1 3.99 0.896 0.000 0.000030 ENSG00000164398 ACSL6 4.64 2.353 0.000 0.000030 ENSG00000165443 PHYHIPL 5.03 1.62 0.000 0.000030 ENSG00000170941 AC135352.1 4.99 2.142 0.000 0.000030 ENSG00000182326 C1S 2.77 0.976 0.000 0.000030 ENSG00000188906 LRRK2 7.76 1.085 0.000 0.000030 ENSG00000198874 TYW1 4.54 1.754 0.000 0.000040 ENSG00000073910 FRY 6.26 2.104 0.000 0.000040 ENSG00000104419 NDRG1 7.3 1.434 0.000 0.000040 ENSG00000130066 SAT1 4.96 1.985 0.000 0.000040 ENSG00000132436 FIGNL1 3.52 0.689 0.000 0.000040 ENSG00000143226 FCGR2A 4.62 1.31 0.000 0.000040 ENSG00000143320 CRABP2 5.93 4.882 0.000 0.000040 ENSG00000156298 TSPAN7 5.53 2.923 0.000 0.000040 ENSG00000160862 AZGP1 6.28 2.132 0.000 0.000040 ENSG00000163638 ADAMTS9 4.94 1.336 0.000 0.000040 ENSG00000189164 ZNF527 6.19 1.071 0.000 0.000050 ENSG00000105649 RAB3A 5.66 1.003 0.000 0.000050 ENSG00000136002 ARHGEF4 294
E. Exon Array Data Appendix Average expression across samples Fold-change p-value FDR Ensembl Gene ID Symbol 6.21 1.475 0.000 0.000050 ENSG00000136243 NUPL2 5.64 0.992 0.000 0.000050 ENSG00000151093 OXSM 4.85 1.082 0.000 0.000050 ENSG00000155629 PIK3AP1 7.07 0.716 0.000 0.000050 ENSG00000157778 PSMG3 8.48 1.368 0.000 0.000050 ENSG00000162545 CAMK2N1 4.72 1.871 0.000 0.000050 ENSG00000164741 DLC1 5.24 1.051 0.000 0.000060 ENSG00000058866 DGKG 5.61 1.415 0.000 0.000060 ENSG00000073464 CLCN4 9.27 0.763 0.000 0.000060 ENSG00000086232 EIF2AK1 3.97 2.144 0.000 0.000060 ENSG00000108176 DNAJC12 7.3 1.402 0.000 0.000060 ENSG00000112852 PCDHB2 4.68 1.736 0.000 0.000060 ENSG00000137393 RNF144B 6.16 1.387 0.000 0.000070 ENSG00000116574 RHOU 8.42 1.11 0.000 0.000070 ENSG00000124226 RNF114 5.72 0.79 0.000 0.000070 ENSG00000129282 MRM1 6 1.143 0.000 0.000070 ENSG00000159228 CBR1 7.25 1.234 0.000 0.000070 ENSG00000166770 AC004696.2 6.42 0.938 0.000 0.000070 ENSG00000172840 PDP2 6.38 0.76 0.000 0.000070 ENSG00000174672 BRSK2 7.22 0.934 0.000 0.000070 ENSG00000179304 FAM156B 6.01 2.099 0.000 0.000070 ENSG00000182217 HIST2H4B 6.01 2.099 0.000 0.000070 ENSG00000183941 HIST2H4A 7.93 2.197 0.000 0.000070 ENSG00000196532 HIST1H3C 6.17 0.703 0.000 0.000070 ENSG00000196741 CXorf24 4.98 1.47 0.000 0.000070 ENSG00000214106 AC093726.6 5.49 0.968 0.000 0.000080 ENSG00000036672 USP2 5.53 1.341 0.000 0.000080 ENSG00000088035 ALG6 5.15 1.343 0.000 0.000080 ENSG00000156500 FAM122C 5.74 1.177 0.000 0.000080 ENSG00000163884 KLF15 6.04 1.258 0.000 0.000080 ENSG00000166402 TUB 7.17 0.939 0.000 0.000080 ENSG00000182646 FAM156A 6.64 4.408 0.000 0.000080 ENSG00000250349 RP5-972B16.2 6.97 0.713 0.000 0.000090 ENSG00000101189 C20orf20 3.92 1.212 0.000 0.000090 ENSG00000119514 GALNT12 3.71 0.824 0.000 0.000090 ENSG00000125804 FAM182A 7.55 0.989 0.000 0.000090 ENSG00000163156 SCNM1 3.42 1.18 0.000 0.000090 ENSG00000181016 C7orf53 6.35 0.891 0.000 0.000090 ENSG00000184205 TSPYL2 4.35 1.373 0.000 0.000090 ENSG00000189283 FHIT 5.51 1.475 0.000 0.000090 ENSG00000198270 TMEM116 7.84 1.309 0.000 0.000100 ENSG00000101224 CDC25B 5.52 0.686 0.000 0.000100 ENSG00000126950 TMEM35 4.4 2.366 0.000 0.000100 ENSG00000148735 PLEKHS1 5.04 1.951 0.000 0.000100 ENSG00000163644 PPM1K 7.83 1.683 0.000 0.000100 ENSG00000172115 CYCS 5.24 1.512 0.000 0.000100 ENSG00000204807 FAM27E2 6.23 1.594 0.000 0.000100 ENSG00000251369 AC003682.1 6.76 1.991 0.000 0.000100 ENSG00000255986 MT1JP 5.41 1.122 0.000 0.000110 ENSG00000131242 RAB11FIP4 7.78 0.733 0.000 0.000110 ENSG00000146676 PURB 6.69 2.507 0.000 0.000110 ENSG00000149294 NCAM1 4.24 0.751 0.000 0.000110 ENSG00000175697 GPR156 4.15 0.854 0.000 0.000110 ENSG00000214290 C11orf93 4.27 1.558 0.000 0.000120 ENSG00000082482 KCNK2 4.89 0.887 0.000 0.000120 ENSG00000100307 CBX7 2.71 0.772 0.000 0.000120 ENSG00000146856 AGBL3 5.69 0.606 0.000 0.000120 ENSG00000169136 ATF5 4.36 0.938 0.000 0.000120 ENSG00000175170 FAM182B 6.37 0.774 0.000 0.000120 ENSG00000255098 RP11-481A20.11 3.52 1.432 0.000 0.000130 ENSG00000003147 ICA1 4.87 1.498 0.000 0.000130 ENSG00000007944 MYLIP 5.81 0.772 0.000 0.000130 ENSG00000101104 PABPC1L 5 1.218 0.000 0.000130 ENSG00000102362 SYTL4 6.13 1.354 0.000 0.000130 ENSG00000158186 MRAS 4.22 0.902 0.000 0.000130 ENSG00000176273 SLC35G1 6.5 1.029 0.000 0.000130 ENSG00000256073 C21orf119 5.73 2.686 0.000 0.000140 ENSG00000117602 RCAN3 7.14 1.232 0.000 0.000140 ENSG00000141753 IGFBP4 5.52 0.559 0.000 0.000140 ENSG00000149599 DUSP15 4.73 1.741 0.000 0.000140 ENSG00000154734 ADAMTS1 3.69 1.648 0.000 0.000150 ENSG00000064225 ST3GAL6 5.21 1.771 0.000 0.000150 ENSG00000106004 HOXA5 6.07 1.193 0.000 0.000150 ENSG00000111364 DDX55 6.02 1.5 0.000 0.000150 ENSG00000120318 ARAP3 5.89 0.804 0.000 0.000150 ENSG00000178809 TRIM73 7.59 0.945 0.000 0.000150 ENSG00000184371 CSF1 295
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Transcriptional Characterization of
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This dissertation is my own work an
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Acknowledgements I would like to th
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5.9 External Dataset Expression Cor
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Introduction 1
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1.1 Glial Cells in the Central Nerv
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1.2 Glioblastoma Multiforme Introdu
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1.3 Primary and Secondary Glioblast
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1.4 Pathways Involved in Glioblasto
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1.5 Pathway Crosstalk Introduction
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Chapter 2 Neurogenesis Contents 2.1
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2.1 Radial Glia Introduction VZ adj
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2.2 Neural Stem Cells Introduction
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Chapter 3 Brain Cancer Stem Cells C
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3.1 The Cancer Stem Cell Hypothesis
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3.1 The Cancer Stem Cell Hypothesis
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3.2 Brain Cancer Stem Cells Introdu
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3.3 Glioma Culture Systems Introduc
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Chapter 4 The Non-Coding RNA World
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4.1 MicroRNA regulation Introductio
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4.1 MicroRNA regulation Introductio
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4.2 Target Prediction and Validatio
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Methods 93
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5.1 Tag-sequencing Data Processing
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5.1 Tag-sequencing Data Processing
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5.2 Array Comparative Genomic Hybri
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5.4 Quantitative Real Time-PCR Vali
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5.5 Literature Mining Methods Figur
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5.5 Literature Mining Methods How m
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5.6 Differential Isoform Expression
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5.9 External Dataset Expression Cor
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5.10 Glioblastoma Pathway Construct
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5.11 MicroRNA Target Prediction Ana
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Results 119
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6.2 Tag mapping Results Table 6.1:
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6.2 Tag mapping Results 123 Figure
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6.3 Copy Number Aberrations Results
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6.3 Copy Number Aberrations Results
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6.4 Core Differentially Expressed G
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6.5 Large-scale qRT-PCR Validation
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6.6 Literature Mining for Different
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6.7 Isoform Differential Expression
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6.8 Long ncRNA Differential Express
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6.8 Long ncRNA Differential Express
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Chapter 7 Dataset Correlation Analy
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7.1 Enrichment Analysis Results Tab
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7.1 Enrichment Analysis Results Fig
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7.1 Enrichment Analysis Results Tab
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7.2 Glioblastoma Expression Signatu
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7.3 Tumour Expression Correlation R
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7.4 Survival Analysis Results Table
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7.4 Survival Analysis Results 867 g
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7.5 Glioblastoma Pathway Analysis R
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8.1 Principles Results say, this is
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8.3 Databases Results Figure 8.1: O
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8.3 Databases Results Figure 8.3: W
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8.4 Filters Results Bayesian method
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8.5 Target Prediction Ensemble Anal
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9.1. Digital Profiling of GNS Cell
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9.2. MicroRNA Target Prediction Ana
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9.3. Concluding Remarks Appendix pr
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A.1 Differential Expression Appendi
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