Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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A.1 Differential Expression Appendix Gene symbol(s) Entrez gene ID(s) Ensembl 56 gene ID(s) Differential expression results Normalised tag counts log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660 KCNA2 3737 ENSG00000177301 Inf 4.29E-04 1.58E-02 149.2 103.9 0.0 2.4 0.0 0.0 KCNJ12 3768 ENSG00000184185 Inf 4.57E-05 2.44E-03 60.5 139.1 0.0 0.0 0.0 0.0 KCNK1 3775 ENSG00000135750 5.95 1.82E-03 4.72E-02 0.0 0.0 90.8 3.3 0.0 1.0 KCNK12 56660 ENSG00000184261 -Inf 1.37E-03 3.79E-02 0.0 0.0 0.0 0.0 39.5 6.8 KCNMB2 10242 ENSG00000197584 5.32 1.85E-05 1.19E-03 2.6 0.0 38.9 204.5 0.0 4.5 KCTD12 115207 ENSG00000178695 -4.06 2.20E-06 1.97E-04 105.3 71.6 25.5 58.7 1598.8 150.0 KIAA1217 56243 ENSG00000120549 4.49 1.62E-03 4.29E-02 35.7 52.3 81.5 4.0 0.0 3.6 KLF6 1316 ENSG00000067082 4.56 5.25E-04 1.80E-02 58.2 113.0 67.2 0.0 0.0 5.4 L3MBTL4 91133 ENSG00000154655 Inf 2.11E-10 4.97E-08 58.0 67.9 11.6 341.6 0.0 0.0 LAMA2 3908 ENSG00000196569 -5.21 3.06E-08 4.42E-06 47.3 25.2 8.0 2.6 730.2 149.0 LAMA4 3910 ENSG00000112769 2.81 2.23E-03 5.43E-02 885.8 984.7 31.7 116.1 38.0 69.6 LEMD1 93273 ENSG00000186007 2.85 3.79E-04 1.43E-02 0.0 6.3 630.6 4.1 0.0 58.9 LFNG 3955 ENSG00000106003 -2.21 2.21E-03 5.38E-02 66.1 96.7 6.9 49.2 429.5 42.4 LGALS3 3958 ENSG00000131981 2.80 1.27E-03 3.56E-02 2898.0 3802.5 3936.6 643.9 219.8 578.3 LHFPL3 375612 ENSG00000187416 Inf 2.25E-09 4.29E-07 485.5 402.6 0.0 0.0 0.0 0.0 LIF 3976 ENSG00000128342 3.97 5.11E-06 3.99E-04 25.7 28.0 98.9 891.5 15.9 27.3 LIFR 3977 ENSG00000113594 -2.95 1.06E-03 3.15E-02 181.0 124.8 38.0 727.7 1803.6 2775.9 LINGO1 84894 ENSG00000169783 5.52 9.07E-04 2.74E-02 113.3 139.7 0.0 0.0 0.0 2.0 LMO2 4005 ENSG00000135363 -4.82 2.89E-06 2.50E-04 20.3 21.2 0.0 4.9 134.6 369.0 LMO3 55885 ENSG00000048540 -Inf 3.43E-11 1.02E-08 0.0 0.0 0.0 0.0 136.9 446.0 LMO4 8543 ENSG00000143013 3.80 6.59E-06 5.03E-04 553.8 1311.2 455.5 1149.8 16.7 122.5 LNX1 84708 ENSG00000072201 4.67 2.34E-03 5.61E-02 2.7 3.1 12.6 101.0 0.0 3.0 LOC283070,CAMK1D 283070,57118 ENSG00000183049 -2.40 5.40E-04 1.84E-02 109.8 142.2 0.6 35.0 578.0 52.7 LOXL4 84171 ENSG00000138131 4.94 1.10E-04 5.09E-03 186.4 184.3 32.9 15.6 0.0 4.7 LPAR6 10161 ENSG00000139679 -3.62 1.24E-04 5.61E-03 29.8 33.8 39.6 0.0 395.9 211.3 LPHN2 23266 ENSG00000117114 -2.05 2.04E-03 5.09E-02 268.8 205.3 10.0 12.7 446.7 183.5 LRAT 9227 ENSG00000121207 5.42 6.40E-06 4.93E-04 0.0 0.0 1.9 290.9 1.5 3.0 LRP4 4038 ENSG00000134569 -2.68 2.41E-03 5.73E-02 29.6 38.9 5.6 18.6 187.5 86.0 LRRC2 79442 ENSG00000163827 Inf 4.14E-06 3.38E-04 0.0 0.0 169.1 0.0 0.0 0.0 LRRC55 219527 ENSG00000183908 -Inf 1.89E-03 4.84E-02 0.0 0.0 0.0 0.0 0.0 49.6 LRRN2 10446 ENSG00000170382 -4.91 1.54E-04 6.71E-03 7.8 5.5 0.0 0.0 97.9 27.3 LTF 4057 ENSG00000012223 Inf 2.03E-07 2.47E-05 0.0 0.0 222.4 0.0 0.0 0.0 LUM 4060 ENSG00000139329 -4.26 6.32E-05 3.23E-03 0.0 0.0 110.9 0.0 507.4 897.7 LXN 56925 ENSG00000079257 -5.76 8.55E-05 4.15E-03 0.0 0.0 0.0 3.7 139.4 9.0 LY96 23643 ENSG00000154589 7.53 1.62E-07 2.01E-05 3.4 59.4 106.5 115.6 0.0 1.0 LYST 1130 ENSG00000143669 5.22 1.71E-07 2.10E-05 85.4 117.1 79.3 454.5 10.3 1.0 MACROD2 140733 ENSG00000172264 -3.07 2.85E-03 6.53E-02 20.6 21.8 0.0 0.0 90.0 33.4 MAF 4094 ENSG00000178573 -4.79 1.41E-05 9.55E-04 14.9 7.1 16.0 0.0 282.4 150.4 MAL 4118 ENSG00000172005 6.24 2.59E-10 5.83E-08 22.8 23.3 11.9 655.2 0.0 6.0 MALL 7851 ENSG00000144063 4.75 3.34E-08 4.77E-06 0.0 0.0 0.0 1117.4 5.4 22.2 MAN1C1 57134 ENSG00000117643 3.59 3.15E-05 1.79E-03 556.5 478.6 107.6 378.3 7.6 45.2 MAP3K5 4217 ENSG00000197442 5.06 1.46E-05 9.83E-04 43.3 28.1 110.6 178.0 5.0 1.0 MAP6 4135 ENSG00000171533 -3.25 1.78E-04 7.62E-03 2.3 32.9 0.6 111.4 629.4 288.0 MAP7 9053 ENSG00000135525 4.45 6.64E-04 2.17E-02 0.0 1.6 25.8 139.8 0.0 5.0 MAPT 4137 ENSG00000186868 4.55 8.34E-06 6.10E-04 353.1 572.9 3.3 34.4 5.3 12.2 MARCH1 55016 ENSG00000145416 6.53 1.27E-04 5.70E-03 18.9 37.1 61.6 41.7 0.0 1.1 MARS 4141 ENSG00000166986 2.80 1.53E-03 4.12E-02 1181.8 771.8 272.0 1.3 39.5 60.2 MARVELD3 91862 ENSG00000140832 -Inf 3.77E-04 1.42E-02 0.3 0.0 0.0 0.0 57.1 3.3 MATN2 4147 ENSG00000132561 3.44 4.46E-04 1.62E-02 326.2 720.9 35.9 6.6 22.8 24.1 MBP 4155 ENSG00000197971 6.47 7.66E-12 2.71E-09 118.6 402.5 103.3 303.0 0.0 6.3 MEIS2 4212 ENSG00000134138 3.05 6.37E-04 2.11E-02 69.3 85.9 36.6 331.3 0.0 36.3 MEST 4232 ENSG00000106484 -2.13 3.82E-03 8.25E-02 1932.6 895.3 66.5 334.9 1665.0 2122.4 242
A.1 Differential Expression Appendix Gene symbol(s) Entrez gene ID(s) Ensembl 56 gene ID(s) Differential expression results Normalised tag counts log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660 MET 4233 ENSG00000105976 9.09 1.36E-18 1.01E-14 1.4 0.0 43.8 9851.7 12.2 0.0 MFAP2 4237 ENSG00000117122 -3.26 2.73E-03 6.32E-02 12.0 6.2 124.4 55.3 3.4 1174.2 MGC87042 256227 ENSG00000105889 Inf 4.14E-03 8.76E-02 65.1 67.1 1.3 0.0 0.0 0.0 MGLL 11343 ENSG00000074416 5.05 1.96E-04 8.25E-03 191.4 165.8 30.8 17.4 2.6 2.0 MIA 8190 ENSG00000213054 5.64 5.51E-04 1.87E-02 21.5 151.9 0.0 0.0 0.0 2.0 MICA 4276 ENSG00000204520 3.69 1.56E-05 1.03E-03 0.0 3.1 1713.4 98.0 65.6 28.8 MICB 4277 ENSG00000204516 4.20 4.73E-03 9.68E-02 0.0 0.0 27.2 85.6 0.0 4.0 MID1IP1 58526 ENSG00000165175 6.08 8.98E-04 2.72E-02 12.1 1.6 101.3 0.0 0.0 1.0 MIPOL1 145282 ENSG00000151338 -Inf 7.14E-04 2.27E-02 0.0 0.0 0.0 0.0 6.3 54.5 MKI67 4288 ENSG00000148773 -Inf 2.65E-04 1.06E-02 0.0 0.0 0.0 0.0 63.7 0.0 MLC1 23209 ENSG00000100427 -2.52 6.39E-04 2.11E-02 207.8 109.7 22.5 12.3 495.8 59.5 MLPH 79083 ENSG00000115648 2.92 2.65E-03 6.15E-02 0.0 0.0 27.7 267.6 1.5 24.7 MMP17 4326 ENSG00000198598 3.58 1.55E-05 1.03E-03 1173.5 864.3 422.6 340.8 5.1 84.8 MMP7 4316 ENSG00000137673 5.74 1.01E-04 4.75E-03 0.0 0.0 17.5 146.3 0.0 2.3 MMRN1 22915 ENSG00000138722 -8.80 1.01E-08 1.65E-06 0.0 0.0 1.3 0.0 279.4 93.2 MN1 4330 ENSG00000169184 -7.23 1.51E-09 3.03E-07 21.6 4.2 0.6 0.0 146.8 384.1 MOCOS 55034 ENSG00000075643 4.47 3.85E-06 3.16E-04 14.1 75.8 201.7 195.0 0.0 14.0 MOSC2 54996 ENSG00000117791 4.40 1.96E-04 8.25E-03 39.5 69.7 77.7 77.9 0.0 7.1 MT1A 4489 ENSG00000205362 Inf 7.71E-04 2.40E-02 1.8 17.4 41.7 25.4 0.0 0.0 MT2A 4502 ENSG00000125148 4.13 2.03E-05 1.28E-03 2039.2 1924.4 8308.0 5237.5 285.0 301.4 MTTP 4547 ENSG00000138823 -3.36 8.32E-04 2.54E-02 6.5 6.3 7.2 27.0 249.5 25.2 MX1 4599 ENSG00000157601 7.05 5.50E-06 4.28E-04 45.1 82.6 86.3 31.8 0.0 0.9 MXRA5 25878 ENSG00000101825 -3.18 1.27E-03 3.56E-02 46.1 23.4 0.0 23.0 123.2 158.0 MYBL1 4603 ENSG00000185697 3.44 4.68E-05 2.49E-03 87.8 81.2 162.7 765.9 17.4 44.4 MYC 4609 ENSG00000136997 3.95 7.75E-06 5.72E-04 155.1 341.8 478.0 32.0 11.4 24.8 MYH3 4621 ENSG00000109063 -4.54 2.06E-05 1.30E-03 18.9 17.2 16.5 51.9 11.8 1298.9 MYL1 4632 ENSG00000168530 -Inf 1.75E-08 2.74E-06 0.0 0.0 0.0 0.0 6.6 310.5 MYL9 10398 ENSG00000101335 -3.85 8.93E-05 4.28E-03 3.8 3.1 110.0 8.5 796.2 370.3 MYO1B 4430 ENSG00000128641 -3.03 1.10E-03 3.19E-02 13.5 0.0 55.3 111.5 514.9 387.9 NAMPT 10135 ENSG00000105835 2.92 5.09E-04 1.77E-02 499.3 678.3 484.4 1970.5 117.5 158.3 NBL1 4681 ENSG00000158747 2.84 7.32E-04 2.32E-02 584.5 491.1 763.1 2068.2 156.4 151.9 NCALD 83988 ENSG00000104490 -2.50 4.45E-03 9.25E-02 53.2 51.5 0.0 4.9 86.7 126.4 NCAM1 4684 ENSG00000149294 3.13 8.63E-04 2.63E-02 3171.6 3747.4 36.2 1733.8 232.8 187.5 NDE1 54820 ENSG00000072864 3.42 4.84E-04 1.72E-02 195.9 200.2 200.6 102.0 24.5 6.9 NDN 4692 ENSG00000182636 -3.46 4.28E-05 2.32E-03 105.3 84.2 0.0 0.0 214.4 405.4 NEFM 4741 ENSG00000104722 -Inf 1.35E-10 3.34E-08 0.0 0.0 0.0 0.0 0.0 536.3 NELL2 4753 ENSG00000184613 -3.24 2.99E-04 1.17E-02 117.2 174.9 0.7 378.4 1070.5 2418.9 NFASC 23114 ENSG00000163531 5.94 2.04E-03 5.08E-02 16.7 25.2 11.9 56.8 0.0 1.0 NFATC2 4773 ENSG00000101096 Inf 1.18E-03 3.37E-02 74.3 83.5 4.4 0.0 0.0 0.0 NFE2L3 9603 ENSG00000050344 3.89 1.43E-04 6.37E-03 43.2 51.1 49.9 215.7 0.0 14.3 NFIA 4774 ENSG00000162599 2.95 3.06E-03 6.87E-02 220.0 429.2 10.7 9.8 1.5 37.4 NID1 4811 ENSG00000116962 2.90 4.46E-04 1.62E-02 954.4 470.8 328.9 2577.4 96.8 204.4 NKX2-1 7080 ENSG00000136352 -5.52 1.01E-08 1.65E-06 4.1 17.2 0.0 0.0 425.3 103.6 NKX6-2 84504 ENSG00000148826 -Inf 1.47E-03 4.02E-02 0.0 0.0 0.0 0.0 0.0 52.2 NLGN4X 57502 ENSG00000146938 3.12 4.96E-04 1.75E-02 570.9 700.9 8.1 162.0 8.4 58.2 NMU 10874 ENSG00000109255 4.32 5.32E-04 1.82E-02 8.1 20.7 153.8 8.9 0.0 6.1 NNAT 4826 ENSG00000053438 -Inf 4.86E-09 8.40E-07 0.0 0.0 0.0 0.0 0.0 363.2 NNMT 4837 ENSG00000166741 3.74 6.59E-06 5.03E-04 519.9 172.4 918.1 175.6 15.2 47.4 NOP16 51491 ENSG00000048162 2.60 1.91E-03 4.86E-02 305.8 448.6 493.2 198.3 57.0 67.7 NOTCH3 4854 ENSG00000074181 -4.24 5.14E-04 1.78E-02 0.0 0.0 0.0 25.1 0.0 317.9 NOV 4856 ENSG00000136999 Inf 4.28E-06 3.47E-04 265.6 174.9 9.8 0.0 0.0 0.0 NPFFR2 10886 ENSG00000056291 -Inf 9.86E-09 1.65E-06 0.0 0.0 0.0 0.0 250.3 5.0 243
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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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7.5 Glioblastoma Pathway Analysis R
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E. Exon Array Data Appendix Average
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F. MicroRNA Array Data Appendix Tab
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F. MicroRNA Array Data Appendix GNS
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F. MicroRNA Array Data Appendix GNS
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Ln Natural logarithm LOH Loss of He
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3.3 Schematisation of cell cycle ph
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8.3 Workflows at the core of the pr
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7.1 Selected Gene Ontology terms an
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