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 5.66 -1.108 0.000 0.000010 ENSG00000135299 ANKRD6 6.65 -2.293 0.000 0.000010 ENSG00000139211 AMIGO2 6.01 -0.834 0.000 0.000010 ENSG00000143466 IKBKE 6.94 -1.227 0.000 0.000010 ENSG00000143772 ITPKB 5.93 -3.525 0.000 0.000010 ENSG00000147459 DOCK5 7.08 -1.588 0.000 0.000010 ENSG00000149269 PAK1 4.75 -1.397 0.000 0.000010 ENSG00000149948 HMGA2 8.76 -2.143 0.000 0.000010 ENSG00000150551 LYPD1 5.98 -1.944 0.000 0.000010 ENSG00000150687 PRSS23 8.52 -1.26 0.000 0.000010 ENSG00000150938 CRIM1 7.07 -1.701 0.000 0.000010 ENSG00000151474 FRMD4A 7.81 -1.827 0.000 0.000010 ENSG00000152104 PTPN14 7.53 -1.628 0.000 0.000010 ENSG00000153707 PTPRD 6.11 -1.021 0.000 0.000010 ENSG00000166016 ABTB2 6.79 -1.103 0.000 0.000010 ENSG00000166444 ST5 6.42 -0.938 0.000 0.000010 ENSG00000168140 VASN 6.31 -1.634 0.000 0.000010 ENSG00000171533 MAP6 6.1 -1.588 0.000 0.000010 ENSG00000171843 MLLT3 7.3 -1.553 0.000 0.000010 ENSG00000172175 MALT1 7.77 -1.621 0.000 0.000010 ENSG00000172638 EFEMP2 7.19 -1.756 0.000 0.000010 ENSG00000173848 NET1 6 -1.068 0.000 0.000010 ENSG00000180592 SKIDA1 6.47 -1.659 0.000 0.000010 ENSG00000182985 CADM1 6.33 -2.532 0.000 0.000010 ENSG00000187720 THSD4 9.32 -1.343 0.000 0.000010 ENSG00000188042 ARL4C 7.93 -1.344 0.000 0.000010 ENSG00000197702 PARVA 9.34 -1.438 0.000 0.000020 ENSG00000002586 CD99 7.95 -1.593 0.000 0.000020 ENSG00000065923 SLC9A7 5.65 -1.606 0.000 0.000020 ENSG00000071205 ARHGAP10 7.14 -1.517 0.000 0.000020 ENSG00000072401 UBE2D1 7.46 -1.853 0.000 0.000020 ENSG00000085377 PREP 6.82 -1.943 0.000 0.000020 ENSG00000103460 TOX3 9.2 -1.742 0.000 0.000020 ENSG00000112972 HMGCS1 5.82 -1.582 0.000 0.000020 ENSG00000114861 FOXP1 7.28 -0.983 0.000 0.000020 ENSG00000128739 SNRPN 7.58 -1.104 0.000 0.000020 ENSG00000129474 AJUBA 5.5 -1.192 0.000 0.000020 ENSG00000129682 FGF13 7.08 -1.836 0.000 0.000020 ENSG00000137942 FNBP1L 8.55 -1.31 0.000 0.000020 ENSG00000154380 ENAH 5.64 -2.757 0.000 0.000020 ENSG00000165659 DACH1 9.13 -1.323 0.000 0.000020 ENSG00000166033 HTRA1 7.58 -2.2 0.000 0.000020 ENSG00000168672 FAM84B 7.44 -1.906 0.000 0.000020 ENSG00000170175 CHRNB1 7.08 -0.917 0.000 0.000020 ENSG00000182197 EXT1 4.37 -1.48 0.000 0.000020 ENSG00000183778 B3GALT5 7.62 -3.42 0.000 0.000020 ENSG00000187955 COL14A1 10.42 -1.09 0.000 0.000020 ENSG00000196924 FLNA 3.77 -1.626 0.000 0.000020 ENSG00000203995 ZYG11A 8.82 -1.245 0.000 0.000020 ENSG00000213625 LEPROT 7.54 -1.127 0.000 0.000020 ENSG00000250588 IQCJ-SCHIP1 4.94 -1.757 0.000 0.000020 ENSG00000255994 C14orf162 8.77 -1.205 0.000 0.000030 ENSG00000065150 IPO5 7.74 -1.274 0.000 0.000030 ENSG00000073712 FERMT2 6.31 -1.635 0.000 0.000030 ENSG00000100592 DAAM1 8.63 -1.933 0.000 0.000030 ENSG00000125266 EFNB2 6.64 -3.548 0.000 0.000030 ENSG00000126010 GRPR 7.09 -4.473 0.000 0.000030 ENSG00000132429 POPDC3 8.83 -0.845 0.000 0.000030 ENSG00000137076 TLN1 5.45 -1.938 0.000 0.000030 ENSG00000137831 UACA 9.29 -1.364 0.000 0.000030 ENSG00000138448 ITGAV 7.34 -2.1 0.000 0.000030 ENSG00000139687 RB1 7.03 -2.562 0.000 0.000030 ENSG00000145536 ADAMTS16 8.41 -1.569 0.000 0.000030 ENSG00000148484 RSU1 7.15 -0.853 0.000 0.000030 ENSG00000150457 LATS2 7.54 -1.712 0.000 0.000030 ENSG00000153976 HS3ST3A1 6.68 -2.064 0.000 0.000030 ENSG00000154556 SORBS2 5.6 -1.892 0.000 0.000030 ENSG00000166450 PRTG 7 -1.416 0.000 0.000030 ENSG00000169047 IRS1 5.16 -1.289 0.000 0.000030 ENSG00000183840 GPR39 6.2 -1.112 0.000 0.000030 ENSG00000203772 SPRN 6.92 -0.86 0.000 0.000040 ENSG00000013364 MVP 6.65 -1.951 0.000 0.000040 ENSG00000069869 NEDD4 5.28 -1.552 0.000 0.000040 ENSG00000079102 RUNX1T1 6.07 -1.116 0.000 0.000040 ENSG00000085741 WNT11 6.6 -1.686 0.000 0.000040 ENSG00000099284 H2AFY2 7.93 -1.989 0.000 0.000040 ENSG00000101670 LIPG 288
E. Exon Array Data Appendix Average expression across samples Fold-change p-value FDR Ensembl Gene ID Symbol 6.88 -0.837 0.000 0.000040 ENSG00000107758 PPP3CB 7.91 -1.277 0.000 0.000040 ENSG00000128829 EIF2AK4 8.37 -0.912 0.000 0.000040 ENSG00000136478 TEX2 6.12 -1.235 0.000 0.000040 ENSG00000137502 RAB30 7.56 -1.128 0.000 0.000040 ENSG00000139668 WDFY2 3.8 -1.027 0.000 0.000040 ENSG00000150672 DLG2 7.69 -0.971 0.000 0.000040 ENSG00000163625 WDFY3 10.31 -1.446 0.000 0.000040 ENSG00000168615 ADAM9 7.77 -1.029 0.000 0.000040 ENSG00000181827 RFX7 8.07 -0.637 0.000 0.000040 ENSG00000198752 CDC42BPB 7.51 -0.797 0.000 0.000040 ENSG00000214717 ZBED1 6.19 -1.808 0.000 0.000050 ENSG00000066468 FGFR2 5.66 -2.079 0.000 0.000050 ENSG00000081803 CADPS2 7.49 -0.96 0.000 0.000050 ENSG00000087088 BAX 6.32 -1.122 0.000 0.000050 ENSG00000100968 NFATC4 8.22 -1.297 0.000 0.000050 ENSG00000102893 PHKB 5.64 -1.108 0.000 0.000050 ENSG00000108239 TBC1D12 9 -2.672 0.000 0.000050 ENSG00000112276 BVES 5.95 -2.589 0.000 0.000050 ENSG00000115232 ITGA4 4.59 -1.69 0.000 0.000050 ENSG00000124134 KCNS1 7.48 -2.329 0.000 0.000050 ENSG00000136928 GABBR2 8.18 -1.075 0.000 0.000050 ENSG00000150347 ARID5B 6.01 -2.228 0.000 0.000050 ENSG00000162745 OLFML2B 6.77 -1.239 0.000 0.000050 ENSG00000166073 GPR176 4.66 -3.976 0.000 0.000050 ENSG00000166342 NETO1 4.69 -1.97 0.000 0.000050 ENSG00000172403 SYNPO2 8.1 -0.895 0.000 0.000050 ENSG00000176014 TUBB6 8.3 -1.04 0.000 0.000060 ENSG00000100403 ZC3H7B 7.95 -1.065 0.000 0.000060 ENSG00000143344 RGL1 7.39 -1.509 0.000 0.000060 ENSG00000171862 PTEN 7.99 -0.895 0.000 0.000060 ENSG00000179820 MYADM 8.3 -0.826 0.000 0.000060 ENSG00000187079 TEAD1 5.29 -2.689 0.000 0.000070 ENSG00000101311 FERMT1 9.82 -0.993 0.000 0.000070 ENSG00000104549 SQLE 7.35 -0.867 0.000 0.000070 ENSG00000112655 PTK7 7.33 -0.735 0.000 0.000070 ENSG00000130338 TULP4 10.17 -0.996 0.000 0.000070 ENSG00000131236 CAP1 8.78 -1.538 0.000 0.000070 ENSG00000134824 FADS2 6.55 -0.792 0.000 0.000070 ENSG00000137936 BCAR3 9.79 -0.973 0.000 0.000070 ENSG00000150093 ITGB1 6.93 -1.288 0.000 0.000070 ENSG00000168502 SOGA2 8.38 -1.506 0.000 0.000070 ENSG00000179431 FJX1 8.32 -1.283 0.000 0.000070 ENSG00000197043 ANXA6 5.8 -1.297 0.000 0.000070 ENSG00000198113 TOR4A 7.19 -1.449 0.000 0.000070 ENSG00000205269 TMEM170B 9.7 -1.29 0.000 0.000080 ENSG00000071127 WDR1 7.75 -1.188 0.000 0.000080 ENSG00000073792 IGF2BP2 7.37 -0.762 0.000 0.000080 ENSG00000100139 MICALL1 6.25 -1.627 0.000 0.000080 ENSG00000140557 ST8SIA2 4.93 -2.465 0.000 0.000080 ENSG00000148798 INA 7.75 -1.245 0.000 0.000080 ENSG00000151612 ZNF827 6.56 -1.118 0.000 0.000080 ENSG00000151718 WWC2 7.26 -1.995 0.000 0.000080 ENSG00000174721 FGFBP3 7.34 -1.183 0.000 0.000080 ENSG00000175115 PACS1 7.06 -1.147 0.000 0.000080 ENSG00000182287 AP1S2 7.79 -1.122 0.000 0.000080 ENSG00000187239 FNBP1 6.27 -0.958 0.000 0.000080 ENSG00000229619 AC106722.1 10.55 -1.573 0.000 0.000090 ENSG00000101608 MYL12A 5.59 -1.066 0.000 0.000090 ENSG00000101665 SMAD7 6.15 -1.436 0.000 0.000090 ENSG00000107518 ATRNL1 5.53 -3.929 0.000 0.000090 ENSG00000144227 NXPH2 5.63 -0.965 0.000 0.000090 ENSG00000158246 FAM46B 6.62 -1.761 0.000 0.000090 ENSG00000165323 FAT3 7.74 -1.946 0.000 0.000100 ENSG00000102996 MMP15 8.65 -1.862 0.000 0.000100 ENSG00000104290 FZD3 6.36 -2.28 0.000 0.000100 ENSG00000151136 BTBD11 7.57 -2.996 0.000 0.000100 ENSG00000152661 GJA1 7.28 -0.967 0.000 0.000100 ENSG00000166912 MTMR10 7.44 -1.18 0.000 0.000110 ENSG00000058091 CDK14 8.62 -0.924 0.000 0.000110 ENSG00000073921 PICALM 5.74 -1.788 0.000 0.000110 ENSG00000152128 TMEM163 7.49 -1.413 0.000 0.000110 ENSG00000158966 CACHD1 5.56 -1.457 0.000 0.000110 ENSG00000165449 SLC16A9 3.3 -2.026 0.000 0.000110 ENSG00000170571 EMB 6.66 -0.922 0.000 0.000110 ENSG00000174307 PHLDA3 5.19 -1.959 0.000 0.000110 ENSG00000183691 NOG 289
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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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