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 6.4 0.769 0.000 0.000150 ENSG00000184857 TMEM186 5.64 1.271 0.000 0.000150 ENSG00000198814 GK 4.72 1.253 0.000 0.000150 ENSG00000213903 LTB4R 5.17 1.876 0.000 0.000160 ENSG00000008277 ADAM22 3.51 1.09 0.000 0.000160 ENSG00000118777 ABCG2 5.85 1.024 0.000 0.000160 ENSG00000164048 ZNF589 6.16 0.956 0.000 0.000160 ENSG00000175175 PPM1E 6.99 1.096 0.000 0.000160 ENSG00000232838 PET117 6.64 0.794 0.000 0.000170 ENSG00000102934 PLLP 6.78 0.622 0.000 0.000170 ENSG00000141582 CBX4 8.37 0.573 0.000 0.000170 ENSG00000143543 JTB 3.96 1.576 0.000 0.000170 ENSG00000158315 RHBDL2 6.45 1.095 0.000 0.000170 ENSG00000204524 ZNF805 6.43 1.7 0.000 0.000180 ENSG00000006652 IFRD1 5.02 1.218 0.000 0.000180 ENSG00000092068 SLC7A8 4.53 2.247 0.000 0.000180 ENSG00000152527 PLEKHH2 6.11 1.012 0.000 0.000180 ENSG00000164620 RELL2 5.74 1.411 0.000 0.000180 ENSG00000165795 NDRG2 6.38 2.236 0.000 0.000190 ENSG00000105409 ATP1A3 8.02 1.715 0.000 0.000190 ENSG00000106537 TSPAN13 6.58 1.894 0.000 0.000190 ENSG00000125144 MT1G 5.6 1.454 0.000 0.000190 ENSG00000164684 ZNF704 6.47 0.985 0.000 0.000200 ENSG00000065717 TLE2 3.93 1.031 0.000 0.000200 ENSG00000122862 SRGN 4.01 1.439 0.000 0.000200 ENSG00000137203 TFAP2A 6.21 1.126 0.000 0.000200 ENSG00000178878 APOLD1 5.99 0.934 0.000 0.000200 ENSG00000180953 ST20 8.5 1.354 0.000 0.000200 ENSG00000198743 SLC5A3 5.6 0.559 0.000 0.000200 ENSG00000251357 AP000350.10 7.33 0.633 0.000 0.000210 ENSG00000130733 YIPF2 5.89 0.896 0.000 0.000210 ENSG00000142528 ZNF473 5.73 1.626 0.000 0.000210 ENSG00000143162 CREG1 6.19 0.828 0.000 0.000210 ENSG00000146909 NOM1 5.34 0.95 0.000 0.000210 ENSG00000149150 SLC43A1 3.29 0.995 0.000 0.000210 ENSG00000165923 AGBL2 6.6 0.893 0.000 0.000210 ENSG00000175898 S1PR2 4.07 0.944 0.000 0.000210 ENSG00000188732 FAM221A 7.44 1.401 0.000 0.000210 ENSG00000231997 FAM27D1 5.25 0.581 0.000 0.000220 ENSG00000126583 PRKCG 6.21 1.077 0.000 0.000220 ENSG00000173875 ZNF791 3.79 1.662 0.000 0.000230 ENSG00000071073 MGAT4A 6.82 0.743 0.000 0.000230 ENSG00000106638 TBL2 7.47 1.573 0.000 0.000230 ENSG00000189060 H1F0 6.2 0.673 0.000 0.000240 ENSG00000106404 CLDN15 6.5 0.814 0.000 0.000240 ENSG00000106479 ZNF862 5.81 0.871 0.000 0.000240 ENSG00000106608 URGCP 5.85 0.819 0.000 0.000240 ENSG00000108852 MPP2 6.65 2.284 0.000 0.000240 ENSG00000154096 THY1 9.19 1.685 0.000 0.000240 ENSG00000166986 MARS 6.7 2.826 0.000 0.000240 ENSG00000175445 LPL 7.67 0.515 0.000 0.000240 ENSG00000184787 UBE2G2 5.33 1.325 0.000 0.000240 ENSG00000237198 FAM27E1 3.64 1.397 0.000 0.000240 ENSG00000250305 KIAA1456 7.42 0.921 0.000 0.000250 ENSG00000130254 SAFB2 4.71 0.878 0.000 0.000250 ENSG00000152049 KCNE4 4.05 1.314 0.000 0.000250 ENSG00000175906 ARL4D 3.91 0.779 0.000 0.000250 ENSG00000204086 RPA4 5.35 2.281 0.000 0.000250 ENSG00000205364 MT1M 4.05 1.053 0.000 0.000260 ENSG00000076554 TPD52 8.37 1.379 0.000 0.000260 ENSG00000085662 AKR1B1 8.61 0.814 0.000 0.000260 ENSG00000104687 GSR 6.29 1.082 0.000 0.000260 ENSG00000105926 MPP6 9.84 0.823 0.000 0.000260 ENSG00000146701 MDH2 5.59 0.957 0.000 0.000260 ENSG00000168301 KCTD6 5.9 0.865 0.000 0.000260 ENSG00000174939 ASPHD1 5.92 0.645 0.000 0.000260 ENSG00000204536 CCHCR1 6.69 0.769 0.000 0.000270 ENSG00000106785 TRIM14 6.99 0.808 0.000 0.000270 ENSG00000125875 TBC1D20 5.82 1.073 0.000 0.000270 ENSG00000164742 ADCY1 4.02 1.271 0.000 0.000270 ENSG00000196932 TMEM26 4.66 0.86 0.000 0.000270 ENSG00000197933 ZNF823 6 1.557 0.000 0.000270 ENSG00000198053 SIRPA 5.43 0.934 0.000 0.000270 ENSG00000215897 ZBTB8B 4.79 0.711 0.000 0.000280 ENSG00000124613 ZNF391 6.98 1.247 0.000 0.000280 ENSG00000126368 NR1D1 4.95 0.642 0.000 0.000290 ENSG00000125510 OPRL1 296
E. Exon Array Data Appendix Average expression across samples Fold-change p-value FDR Ensembl Gene ID Symbol 4.21 1.238 0.000 0.000290 ENSG00000166387 PPFIBP2 5.58 0.709 0.000 0.000290 ENSG00000186951 PPARA 7.3 1.284 0.000 0.000290 ENSG00000187372 PCDHB13 3.61 0.734 0.000 0.000290 ENSG00000196167 C11orf92 5.69 1.412 0.000 0.000300 ENSG00000068650 ATP11A 7.51 0.631 0.000 0.000300 ENSG00000106070 GRB10 5.19 0.553 0.000 0.000300 ENSG00000170379 FAM115C 5.03 0.896 0.000 0.000300 ENSG00000257755 orphan 4.33 1.526 0.000 0.000310 ENSG00000104324 CPQ 5.18 0.844 0.000 0.000310 ENSG00000107957 SH3PXD2A 6.49 0.752 0.000 0.000310 ENSG00000114859 CLCN2 7.06 1.16 0.000 0.000310 ENSG00000135457 TFCP2 5.35 1.852 0.000 0.000310 ENSG00000153714 LURAP1L 10.2 0.876 0.000 0.000310 ENSG00000171867 PRNP 3.1 1.481 0.000 0.000320 ENSG00000106560 GIMAP2 7.45 1.354 0.000 0.000320 ENSG00000150893 FREM2 5.65 0.632 0.000 0.000320 ENSG00000163132 MSX1 8 0.759 0.000 0.000320 ENSG00000178741 COX5A 5.45 1.098 0.000 0.000320 ENSG00000211445 GPX3 6.16 0.599 0.000 0.000330 ENSG00000083812 ZNF324 7.47 0.735 0.000 0.000330 ENSG00000145882 PCYOX1L 5.9 0.732 0.000 0.000330 ENSG00000155428 TRIM74 6.82 0.92 0.000 0.000340 ENSG00000106415 GLCCI1 5.56 0.658 0.000 0.000340 ENSG00000116039 ATP6V1B1 4.71 0.686 0.000 0.000340 ENSG00000132801 ZSWIM3 6.32 0.688 0.000 0.000340 ENSG00000134086 VHL 7.86 0.575 0.000 0.000350 ENSG00000113269 RNF130 5.23 1.823 0.000 0.000350 ENSG00000131015 ULBP2 4.27 1.325 0.000 0.000350 ENSG00000197757 HOXC6 7.01 1.393 0.000 0.000350 ENSG00000231360 AL592284.2 3.41 0.946 0.000 0.000360 ENSG00000025423 HSD17B6 5.67 1.773 0.000 0.000360 ENSG00000165118 C9orf64 4.77 0.903 0.000 0.000360 ENSG00000175911 AC127496.1 4.45 1.145 0.000 0.000360 ENSG00000232956 SNHG15 5.73 1.061 0.000 0.000370 ENSG00000135245 HILPDA 6.24 1.297 0.000 0.000370 ENSG00000135472 FAIM2 6.44 0.912 0.000 0.000370 ENSG00000154930 ACSS1 7.65 1.07 0.000 0.000370 ENSG00000168303 MPLKIP 5.48 0.809 0.000 0.000370 ENSG00000205358 MT1H 4.75 1.489 0.000 0.000380 ENSG00000112379 KIAA1244 4.21 1.081 0.000 0.000380 ENSG00000119547 ONECUT2 3.38 0.996 0.000 0.000380 ENSG00000144290 SLC4A10 5.43 0.988 0.000 0.000380 ENSG00000146833 TRIM4 7.01 1.023 0.000 0.000380 ENSG00000173276 ZNF295 8.3 0.683 0.000 0.000380 ENSG00000175193 PARL 4.84 0.881 0.000 0.000390 ENSG00000204856 FAM216A 6.52 1.323 0.000 0.000400 ENSG00000107829 FBXW4 6.84 0.91 0.000 0.000400 ENSG00000124228 DDX27 7.24 0.665 0.000 0.000410 ENSG00000101407 TTI1 6.79 0.747 0.000 0.000410 ENSG00000106245 BUD31 6.3 0.592 0.000 0.000410 ENSG00000142700 DMRTA2 6.5 0.915 0.000 0.000410 ENSG00000189046 ALKBH2 5.51 2.199 0.000 0.000410 ENSG00000215247 5.9 0.698 0.000 0.000420 ENSG00000006194 ZNF263 7.11 1.686 0.000 0.000420 ENSG00000120328 PCDHB12 7.42 0.68 0.000 0.000420 ENSG00000136213 CHST12 5.42 1.536 0.000 0.000420 ENSG00000151364 KCTD14 7.23 0.928 0.000 0.000420 ENSG00000198171 DDRGK1 6.44 0.8 0.000 0.000430 ENSG00000131368 MRPS25 8.34 0.747 0.000 0.000440 ENSG00000111678 C12orf57 6.57 0.838 0.000 0.000440 ENSG00000165661 QSOX2 5.88 1.608 0.000 0.000440 ENSG00000186868 MAPT 5.39 0.894 0.000 0.000440 ENSG00000253293 HOXA10 7.35 0.627 0.000 0.000450 ENSG00000156928 MALSU1 5.28 1.124 0.000 0.000450 ENSG00000172006 ZNF554 4.69 0.646 0.000 0.000450 ENSG00000177335 C8orf31 5.68 1.476 0.000 0.000450 ENSG00000206535 LNP1 6.92 0.94 0.000 0.000460 ENSG00000197608 ZNF841 3.25 1.454 0.000 0.000470 ENSG00000168811 IL12A 4.52 0.897 0.000 0.000470 ENSG00000176593 CTD-2368P22.1 3.63 1.342 0.000 0.000480 ENSG00000113389 NPR3 3.35 1.071 0.000 0.000480 ENSG00000176907 C8orf4 5.37 0.494 0.000 0.000480 ENSG00000177380 PPFIA3 7.44 0.526 0.000 0.000480 ENSG00000229212 RP11-561C5.4 4.52 1.355 0.000 0.000490 ENSG00000120915 EPHX2 4.77 1.002 0.000 0.000490 ENSG00000125388 GRK4 297
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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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Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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