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 6.73 -0.823 0.000 0.000120 ENSG00000011114 BTBD7 6.86 -0.624 0.000 0.000120 ENSG00000037757 MRI1 4.78 -1.277 0.000 0.000120 ENSG00000068781 STON1-GTF2A1L 9.49 -1.337 0.000 0.000120 ENSG00000075213 SEMA3A 4.78 -1.205 0.000 0.000120 ENSG00000108187 PBLD 7.01 -1.596 0.000 0.000120 ENSG00000109586 GALNT7 6.73 -0.668 0.000 0.000120 ENSG00000110237 ARHGEF17 6.37 -1.075 0.000 0.000120 ENSG00000126790 L3HYPDH 6.21 -1.532 0.000 0.000120 ENSG00000165996 PTPLA 6.16 -1.903 0.000 0.000120 ENSG00000180914 OXTR 9.41 -1.204 0.000 0.000120 ENSG00000196576 PLXNB2 5.41 -1.323 0.000 0.000120 ENSG00000197646 PDCD1LG2 6.14 -0.846 0.000 0.000130 ENSG00000090975 PITPNM2 6.87 -0.981 0.000 0.000130 ENSG00000148737 TCF7L2 7.63 -1.404 0.000 0.000130 ENSG00000177508 IRX3 6.23 -2.345 0.000 0.000140 ENSG00000104332 SFRP1 8.2 -1.368 0.000 0.000140 ENSG00000140682 TGFB1I1 7.55 -0.981 0.000 0.000140 ENSG00000148468 FAM171A1 6.12 -0.812 0.000 0.000140 ENSG00000162804 SNED1 7.73 -1.008 0.000 0.000140 ENSG00000196865 NHLRC2 7.36 -1.145 0.000 0.000150 ENSG00000055163 CYFIP2 6.64 -0.859 0.000 0.000150 ENSG00000072422 RHOBTB1 6.33 -1.765 0.000 0.000150 ENSG00000130176 CNN1 8.66 -0.711 0.000 0.000150 ENSG00000130638 ATXN10 8.32 -0.937 0.000 0.000150 ENSG00000139793 MBNL2 5.8 -1.718 0.000 0.000150 ENSG00000173320 STOX2 7.41 -1.382 0.000 0.000150 ENSG00000176788 BASP1 5.41 -4.49 0.000 0.000150 ENSG00000187714 SLC18A3 6.97 -0.57 0.000 0.000160 ENSG00000061273 HDAC7 8.41 -1.415 0.000 0.000160 ENSG00000163430 FSTL1 6.58 -1.178 0.000 0.000160 ENSG00000169436 COL22A1 8.98 -1.848 0.000 0.000170 ENSG00000135048 TMEM2 8.41 -1.185 0.000 0.000170 ENSG00000137710 RDX 4.5 -1.657 0.000 0.000170 ENSG00000154027 AK5 8.87 -0.936 0.000 0.000170 ENSG00000167460 TPM4 7.64 -1.238 0.000 0.000170 ENSG00000182319 PRAGMIN 8.22 -0.609 0.000 0.000170 ENSG00000182534 MXRA7 8.7 -1.291 0.000 0.000170 ENSG00000186575 NF2 7.62 -2.017 0.000 0.000180 ENSG00000084710 EFR3B 7.84 -0.796 0.000 0.000180 ENSG00000108091 CCDC6 8.51 -1.519 0.000 0.000180 ENSG00000148848 ADAM12 9.53 -0.645 0.000 0.000180 ENSG00000168175 MAPK1IP1L 7.32 -1.041 0.000 0.000180 ENSG00000170525 PFKFB3 7.31 -1.108 0.000 0.000180 ENSG00000178764 ZHX2 6.15 -0.992 0.000 0.000190 ENSG00000116675 DNAJC6 6.52 -1.174 0.000 0.000190 ENSG00000131370 SH3BP5 6.08 -0.978 0.000 0.000190 ENSG00000143816 WNT9A 6.26 -1.511 0.000 0.000190 ENSG00000255103 KIAA0754 6.71 -1.362 0.000 0.000200 ENSG00000122335 SERAC1 5.2 -3.22 0.000 0.000200 ENSG00000123119 NECAB1 5.45 -1.76 0.000 0.000200 ENSG00000138696 BMPR1B 6.28 -2.18 0.000 0.000200 ENSG00000146426 TIAM2 8.62 -0.877 0.000 0.000200 ENSG00000152558 TMEM123 6.89 -0.815 0.000 0.000210 ENSG00000068383 INPP5A 7.22 -1.283 0.000 0.000210 ENSG00000105974 CAV1 9.12 -1.876 0.000 0.000210 ENSG00000106484 MEST 7.38 -1.482 0.000 0.000210 ENSG00000113328 CCNG1 6.45 -1.103 0.000 0.000210 ENSG00000119681 LTBP2 6.12 -0.72 0.000 0.000210 ENSG00000132334 PTPRE 6.68 -1.403 0.000 0.000210 ENSG00000188158 NHS 7.53 -0.946 0.000 0.000230 ENSG00000107819 SFXN3 7.73 -0.772 0.000 0.000230 ENSG00000120254 MTHFD1L 7.79 -0.638 0.000 0.000230 ENSG00000122863 CHST3 3.92 -2.068 0.000 0.000230 ENSG00000158164 TMSB15A 7.94 -0.812 0.000 0.000230 ENSG00000185950 IRS2 7.35 -1.124 0.000 0.000240 ENSG00000067064 IDI1 7.4 -0.902 0.000 0.000240 ENSG00000124788 ATXN1 5.98 -0.83 0.000 0.000240 ENSG00000138131 LOXL4 7.87 -1.371 0.000 0.000240 ENSG00000187498 COL4A1 7.87 -0.797 0.000 0.000240 ENSG00000198951 NAGA 4.77 -1.178 0.000 0.000250 ENSG00000100285 NEFH 7.33 -0.837 0.000 0.000250 ENSG00000103335 PIEZO1 8.26 -2.268 0.000 0.000250 ENSG00000132470 ITGB4 8.65 -1.241 0.000 0.000250 ENSG00000181019 NQO1 5.67 -0.561 0.000 0.000250 ENSG00000198832 RP3-412A9.11 6.86 -0.871 0.000 0.000260 ENSG00000070269 C14orf101 290
E. Exon Array Data Appendix Average expression across samples Fold-change p-value FDR Ensembl Gene ID Symbol 5.37 -1.251 0.000 0.000260 ENSG00000113448 PDE4D 7.86 -0.688 0.000 0.000260 ENSG00000139645 ANKRD52 4.6 -1.255 0.000 0.000260 ENSG00000165626 BEND7 6.96 -0.585 0.000 0.000260 ENSG00000182541 LIMK2 6.14 -0.788 0.000 0.000270 ENSG00000014914 MTMR11 8.85 -1.086 0.000 0.000270 ENSG00000064666 CNN2 7.38 -0.682 0.000 0.000270 ENSG00000128283 CDC42EP1 8.39 -1.216 0.000 0.000270 ENSG00000162909 CAPN2 8.41 -0.967 0.000 0.000270 ENSG00000176903 PNMA1 5.62 -1.998 0.000 0.000270 ENSG00000182732 RGS6 6.79 -0.841 0.000 0.000280 ENSG00000151553 FAM160B1 7.41 -1.128 0.000 0.000280 ENSG00000170365 SMAD1 8.41 -1.273 0.000 0.000280 ENSG00000183722 LHFP 3.46 -1.447 0.000 0.000290 ENSG00000022556 NLRP2 2.61 -0.607 0.000 0.000290 ENSG00000133640 LRRIQ1 7.3 -1.36 0.000 0.000300 ENSG00000185339 TCN2 5.04 -1.653 0.000 0.000300 ENSG00000215475 SIAH3 9 -1.175 0.000 0.000310 ENSG00000107779 BMPR1A 8.88 -1.175 0.000 0.000310 ENSG00000117298 ECE1 8.39 -0.598 0.000 0.000310 ENSG00000198954 KIAA1279 5.41 -2.252 0.000 0.000320 ENSG00000124610 HIST1H1A 7.1 -1.379 0.000 0.000320 ENSG00000205726 ITSN1 7.71 -0.927 0.000 0.000330 ENSG00000102753 KPNA3 7 -0.851 0.000 0.000330 ENSG00000143553 SNAPIN 9.78 -0.783 0.000 0.000330 ENSG00000147416 ATP6V1B2 5.61 -2.025 0.000 0.000330 ENSG00000188517 COL25A1 6.51 -2.126 0.000 0.000340 ENSG00000152977 ZIC1 7.7 -0.908 0.000 0.000340 ENSG00000154001 PPP2R5E 4.97 -0.768 0.000 0.000340 ENSG00000203877 RIPPLY2 6.95 -1.345 0.000 0.000350 ENSG00000080298 RFX3 8.79 -1.528 0.000 0.000350 ENSG00000082781 ITGB5 8.19 -0.882 0.000 0.000350 ENSG00000175662 TOM1L2 4.95 -2.667 0.000 0.000360 ENSG00000089472 HEPH 9.11 -1.105 0.000 0.000360 ENSG00000102898 NUTF2 7.58 -1.796 0.000 0.000360 ENSG00000125430 HS3ST3B1 9.2 -1.289 0.000 0.000360 ENSG00000172380 GNG12 6.85 -1.643 0.000 0.000370 ENSG00000139263 LRIG3 8.35 -0.864 0.000 0.000370 ENSG00000165476 REEP3 6.9 -1.305 0.000 0.000380 ENSG00000040199 PHLPP2 8.79 -0.701 0.000 0.000380 ENSG00000120733 KDM3B 5 -1.693 0.000 0.000380 ENSG00000143473 KCNH1 6.27 -2.298 0.000 0.000380 ENSG00000173917 HOXB2 6.76 -0.673 0.000 0.000380 ENSG00000205011 AC073082.1 6.92 -1.127 0.000 0.000390 ENSG00000042493 CAPG 7.91 -0.553 0.000 0.000390 ENSG00000204138 PHACTR4 9.42 -0.581 0.000 0.000400 ENSG00000143742 SRP9 8.05 -1.162 0.000 0.000410 ENSG00000107249 GLIS3 4.6 -0.65 0.000 0.000410 ENSG00000172238 ATOH1 8.33 -1.572 0.000 0.000420 ENSG00000152767 FARP1 4.7 -2.758 0.000 0.000420 ENSG00000163762 TM4SF18 7.29 -1.321 0.000 0.000420 ENSG00000179242 CDH4 4.32 -1.336 0.000 0.000420 ENSG00000188316 ENO4 7.53 -0.977 0.000 0.000430 ENSG00000039560 RAI14 8.64 -1.21 0.000 0.000430 ENSG00000128791 TWSG1 7.73 -1.201 0.000 0.000430 ENSG00000130147 SH3BP4 6.59 -1.229 0.000 0.000440 ENSG00000113721 PDGFRB 7.62 -0.694 0.000 0.000440 ENSG00000150760 DOCK1 7.79 -0.655 0.000 0.000450 ENSG00000148411 NACC2 4.02 -1.254 0.000 0.000450 ENSG00000154760 SLFN13 6.46 -1.117 0.000 0.000450 ENSG00000188153 COL4A5 4.84 -1.145 0.000 0.000460 ENSG00000109339 MAPK10 9.11 -2.027 0.000 0.000460 ENSG00000118523 CTGF 7.55 -1.017 0.000 0.000460 ENSG00000137693 YAP1 7.01 -0.558 0.000 0.000460 ENSG00000186174 BCL9L 6.04 -1.369 0.000 0.000460 ENSG00000197565 COL4A6 7.85 -0.791 0.000 0.000460 ENSG00000198856 OSTC 3.62 -0.988 0.000 0.000470 ENSG00000155974 GRIP1 6.5 -0.997 0.000 0.000470 ENSG00000171055 FEZ2 6.12 -0.539 0.000 0.000470 ENSG00000171680 PLEKHG5 10.02 -1.536 0.000 0.000490 ENSG00000041982 TNC 7.6 -0.459 0.000 0.000490 ENSG00000166454 ATMIN 6.43 -0.794 0.001 0.000500 ENSG00000197261 C6orf141 8.15 -1.104 0.001 0.000510 ENSG00000119655 NPC2 5.83 -1.663 0.001 0.000510 ENSG00000146373 RNF217 3.77 -1.114 0.001 0.000510 ENSG00000150540 HNMT 7.94 -0.855 0.001 0.000510 ENSG00000159842 ABR 291
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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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A.1 Differential Expression Appendi
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