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 7.84 -0.72 0.001 0.000510 ENSG00000214265 SNURF 3.66 -1.512 0.001 0.000510 ENSG00000214919 AC104472.1 5.04 -1.875 0.001 0.000520 ENSG00000102935 ZNF423 6.22 -0.928 0.001 0.000530 ENSG00000106991 ENG 7.3 -0.798 0.001 0.000530 ENSG00000119977 TCTN3 8.03 -1.528 0.001 0.000530 ENSG00000120437 ACAT2 6.41 -1.877 0.001 0.000530 ENSG00000138829 FBN2 3.03 -0.791 0.001 0.000530 ENSG00000162614 NEXN 6.94 -2.214 0.001 0.000540 ENSG00000121005 CRISPLD1 6.77 -1.284 0.001 0.000540 ENSG00000164465 DCBLD1 4.6 -1.496 0.001 0.000540 ENSG00000172671 ZFAND4 5.97 -0.955 0.001 0.000550 ENSG00000162520 SYNC 6.25 -0.89 0.001 0.000550 ENSG00000163485 ADORA1 4.05 -1.925 0.001 0.000550 ENSG00000165983 PTER 7.78 -1.38 0.001 0.000550 ENSG00000180537 RNF182 7.99 -0.599 0.001 0.000560 ENSG00000166333 ILK 5.29 -0.835 0.001 0.000570 ENSG00000139832 RAB20 8.27 -1.102 0.001 0.000580 ENSG00000122026 RPL21 6.95 -0.781 0.001 0.000580 ENSG00000167123 CERCAM 5.84 -2.436 0.001 0.000580 ENSG00000205664 RP11-706O15.1 7.91 -1.209 0.001 0.000590 ENSG00000122884 P4HA1 4.18 -1.509 0.001 0.000590 ENSG00000172716 SLFN11 8.52 -0.9 0.001 0.000600 ENSG00000149485 FADS1 6.61 -0.601 0.001 0.000610 ENSG00000087903 RFX2 5.67 -0.674 0.001 0.000610 ENSG00000095539 SEMA4G 7.5 -0.85 0.001 0.000610 ENSG00000160584 SIK3 7.03 -0.509 0.001 0.000610 ENSG00000166507 NDST2 7.78 -0.812 0.001 0.000620 ENSG00000074181 NOTCH3 6.24 -0.729 0.001 0.000630 ENSG00000157322 CLEC18A 9.2 -1.574 0.001 0.000640 ENSG00000112186 CAP2 7.07 -2.615 0.001 0.000650 ENSG00000087510 TFAP2C 7.91 -0.832 0.001 0.000650 ENSG00000142173 COL6A2 8.58 -0.86 0.001 0.000650 ENSG00000197965 MPZL1 5.92 -0.73 0.001 0.000660 ENSG00000124831 LRRFIP1 6.9 -1.51 0.001 0.000670 ENSG00000104783 KCNN4 3.47 -0.881 0.001 0.000670 ENSG00000146038 DCDC2 5.8 -0.887 0.001 0.000670 ENSG00000198768 APCDD1L 6.88 -0.976 0.001 0.000680 ENSG00000148429 USP6NL 8.6 -1.479 0.001 0.000680 ENSG00000169855 ROBO1 6.76 -0.914 0.001 0.000680 ENSG00000181649 PHLDA2 7.55 -0.953 0.001 0.000690 ENSG00000014216 CAPN1 5.39 -0.948 0.001 0.000690 ENSG00000112183 RBM24 7.14 -0.869 0.001 0.000690 ENSG00000118263 KLF7 7.46 -0.671 0.001 0.000700 ENSG00000148498 PARD3 5.7 -1.198 0.001 0.000710 ENSG00000135824 RGS8 6.54 -1.323 0.001 0.000720 ENSG00000161958 FGF11 6.12 -1.585 0.001 0.000720 ENSG00000172059 KLF11 8.33 -0.669 0.001 0.000720 ENSG00000172081 MOB3A 6.15 -0.95 0.001 0.000720 ENSG00000239887 C1orf226 6.85 -1.301 0.001 0.000730 ENSG00000123096 SSPN 6.8 -0.95 0.001 0.000740 ENSG00000196935 SRGAP1 6.28 -0.714 0.001 0.000750 ENSG00000157335 CLEC18C 6.9 -2.327 0.001 0.000760 ENSG00000146411 SLC2A12 7.01 -1.299 0.001 0.000760 ENSG00000197093 GAL3ST4 7.62 -0.757 0.001 0.000770 ENSG00000137216 TMEM63B 5.99 -1.143 0.001 0.000770 ENSG00000144218 AFF3 8.19 -1.003 0.001 0.000780 ENSG00000173457 PPP1R14B 6.95 -1.347 0.001 0.000790 ENSG00000065534 MYLK 9.56 -1.273 0.001 0.000790 ENSG00000124942 AHNAK 8.75 -1.094 0.001 0.000790 ENSG00000160285 LSS 6.52 -1.65 0.001 0.000790 ENSG00000172469 MANEA 6.01 -0.921 0.001 0.000790 ENSG00000173715 C11orf80 4.28 -1.027 0.001 0.000790 ENSG00000197140 ADAM32 4.65 -1.509 0.001 0.000800 ENSG00000169946 ZFPM2 7.97 -1.128 0.001 0.000800 ENSG00000183098 GPC6 5.92 -1.632 0.001 0.000810 ENSG00000003436 TFPI 7.2 -0.498 0.001 0.000810 ENSG00000070366 SMG6 6.43 -0.515 0.001 0.000830 ENSG00000172346 CSDC2 4.78 -0.836 0.001 0.000830 ENSG00000228120 AP001631.10 8.58 -0.967 0.001 0.000840 ENSG00000145349 CAMK2D 8.74 -0.995 0.001 0.000850 ENSG00000068793 CYFIP1 7.38 -0.478 0.001 0.000850 ENSG00000197324 LRP10 6.39 -0.685 0.001 0.000860 ENSG00000065665 SEC61A2 6.27 -0.754 0.001 0.000860 ENSG00000140839 CLEC18B 4.96 -1.366 0.001 0.000870 ENSG00000150630 VEGFC 7.31 -0.864 0.001 0.000870 ENSG00000151929 BAG3 292
E. Exon Array Data Appendix Average expression across samples Fold-change p-value FDR Ensembl Gene ID Symbol 5.94 -1.001 0.001 0.000870 ENSG00000165406 Mar-08 7.37 -0.827 0.001 0.000880 ENSG00000126773 PCNXL4 8.75 -0.652 0.001 0.000890 ENSG00000138107 ACTR1A 8.13 -0.645 0.001 0.000900 ENSG00000132142 ACACA 2.65 -0.596 0.001 0.000900 ENSG00000151338 MIPOL1 7.65 -2.89 0.001 0.000910 ENSG00000145623 OSMR 4.78 -1.089 0.001 0.000930 ENSG00000164484 TMEM200A 8.17 -0.961 0.001 0.000930 ENSG00000180776 ZDHHC20 6.74 -1.118 0.001 0.000940 ENSG00000165512 ZNF22 3.35 -0.987 0.001 0.000950 ENSG00000174792 C4orf26 6.79 -1.011 0.001 0.000950 ENSG00000183580 FBXL7 7.28 -0.97 0.001 0.000960 ENSG00000109536 FRG1 5.53 -0.609 0.001 0.000960 ENSG00000123191 ATP7B 8.79 -0.678 0.001 0.000960 ENSG00000152022 LIX1L 6.78 -1.182 0.001 0.000960 ENSG00000164251 F2RL1 7.8 -0.836 0.001 0.000970 ENSG00000147100 SLC16A2 7.29 -0.674 0.001 0.000990 ENSG00000130643 CALY 6.22 -0.585 0.001 0.000990 ENSG00000198546 ZNF511 4.79 2.559 0.000 0.000000 ENSG00000005020 SKAP2 5.52 1.043 0.000 0.000000 ENSG00000008056 SYN1 8.25 3.134 0.000 0.000000 ENSG00000010278 CD9 4.2 2.503 0.000 0.000000 ENSG00000064763 FAR2 6.63 0.942 0.000 0.000000 ENSG00000085117 CD82 4.32 2.793 0.000 0.000000 ENSG00000086300 SNX10 4.71 2.29 0.000 0.000000 ENSG00000087303 NID2 7.32 0.863 0.000 0.000000 ENSG00000105379 ETFB 3.96 1.434 0.000 0.000000 ENSG00000105499 PLA2G4C 3.11 1.41 0.000 0.000000 ENSG00000105889 STEAP1B 5.57 1.454 0.000 0.000000 ENSG00000106789 CORO2A 5.47 1.651 0.000 0.000000 ENSG00000114948 ADAM23 5.72 0.898 0.000 0.000000 ENSG00000119431 HDHD3 7.21 4.479 0.000 0.000000 ENSG00000124785 NRN1 7.81 0.974 0.000 0.000000 ENSG00000128563 PRKRIP1 5.96 1.277 0.000 0.000000 ENSG00000128709 HOXD9 6.11 3.085 0.000 0.000000 ENSG00000128710 HOXD10 5.82 1.922 0.000 0.000000 ENSG00000128713 HOXD11 6.64 1.409 0.000 0.000000 ENSG00000130203 APOE 5.62 4.15 0.000 0.000000 ENSG00000134853 PDGFRA 3.79 1.54 0.000 0.000000 ENSG00000137727 ARHGAP20 5.02 1.678 0.000 0.000000 ENSG00000140022 STON2 5.67 2.034 0.000 0.000000 ENSG00000142494 SLC47A1 7.69 1.182 0.000 0.000000 ENSG00000147883 CDKN2B 4.8 2.142 0.000 0.000000 ENSG00000153029 MR1 3.98 1.624 0.000 0.000000 ENSG00000154493 C10orf90 7.05 1.693 0.000 0.000000 ENSG00000154537 FAM27C 4.8 1.635 0.000 0.000000 ENSG00000156395 SORCS3 5.16 1.341 0.000 0.000000 ENSG00000160179 ABCG1 5.79 2.664 0.000 0.000000 ENSG00000163235 TGFA 3.18 1.87 0.000 0.000000 ENSG00000164647 STEAP1 4.75 1.82 0.000 0.000000 ENSG00000167216 KATNAL2 5.26 2.322 0.000 0.000000 ENSG00000167306 MYO5B 5.67 2.245 0.000 0.000000 ENSG00000168234 TTC39C 5.37 1.902 0.000 0.000000 ENSG00000168779 SHOX2 8.11 1.311 0.000 0.000000 ENSG00000169919 GUSB 7.18 1.878 0.000 0.000000 ENSG00000170215 FAM27B 5.26 1.276 0.000 0.000000 ENSG00000171729 TMEM51 4.33 2.548 0.000 0.000000 ENSG00000173083 HPSE 6.17 1.425 0.000 0.000000 ENSG00000173805 HAP1 6.57 3.093 0.000 0.000000 ENSG00000175197 DDIT3 6.62 3.734 0.000 0.000000 ENSG00000176165 FOXG1 7.24 1.431 0.000 0.000000 ENSG00000178381 ZFAND2A 3.53 1.663 0.000 0.000000 ENSG00000178538 CA8 7.2 1.913 0.000 0.000000 ENSG00000182368 FAM27A 4.39 2.726 0.000 0.000000 ENSG00000186960 C14orf23 7.12 1.148 0.000 0.000000 ENSG00000187244 BCAM 5.4 1.328 0.000 0.000000 ENSG00000187764 SEMA4D 6.42 4.099 0.000 0.000000 ENSG00000189058 APOD 3.76 1.495 0.000 0.000000 ENSG00000196954 CASP4 5.08 1.747 0.000 0.000000 ENSG00000204634 TBC1D8 5.43 1.793 0.000 0.000000 ENSG00000214575 CPEB1 4.75 2.361 0.000 0.000000 ENSG00000223572 CKMT1A 4.81 2.497 0.000 0.000000 ENSG00000237289 CKMT1B 5.34 2.004 0.000 0.000000 ENSG00000258518 AC112502.1 6.52 1.423 0.000 0.000010 ENSG00000003096 KLHL13 5.29 2.135 0.000 0.000010 ENSG00000019549 SNAI2 4.56 1.944 0.000 0.000010 ENSG00000056736 IL17RB 293
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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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Page 281 and 282: Appendix C Long ncRNAs We detected
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Page 295 and 296: E. Exon Array Data Appendix Average
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Page 309 and 310: F. MicroRNA Array Data Appendix Tab
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Page 323 and 324: Bibliography [1] Cell signaling tec
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