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 RP5-955M13.1,KCNG1 3755 ENSG00000026559,ENSG00000242964 3.17 4.85E-03 9.82E-02 31.5 43.7 73.1 75.4 0.0 14.1 RP9 6100 ENSG00000164610 2.59 3.34E-03 7.40E-02 569.1 650.0 335.5 82.3 64.7 53.8 RPSAP52 204010 ENSG00000241749 4.40 2.37E-03 5.66E-02 0.0 0.0 12.2 116.6 0.0 4.2 RRAD 6236 ENSG00000166592 Inf 2.54E-09 4.79E-07 0.0 0.0 84.0 253.0 0.0 0.0 RRP7A 27341 ENSG00000189306 3.00 2.73E-03 6.32E-02 78.1 35.6 263.9 2.0 9.9 15.1 RRS1 23212 ENSG00000179041 4.41 8.14E-04 2.50E-02 72.2 64.0 98.5 0.0 0.0 5.5 RTN1 6252 ENSG00000139970 -5.34 5.31E-07 5.68E-05 8.1 5.5 0.6 19.3 385.7 286.3 RTP4 64108 ENSG00000136514 Inf 7.77E-06 5.72E-04 0.0 0.7 98.1 58.2 0.0 0.0 S100A6 6277 ENSG00000197956 6.04 2.05E-17 5.08E-14 2259.3 324.2 5709.9 512.7 12.3 53.4 S100B 6285 ENSG00000160307 -2.18 5.35E-04 1.83E-02 3679.1 1302.1 6.3 66.5 3663.5 496.5 S1PR3 1903 ENSG00000213694 -4.14 4.96E-03 9.98E-02 29.7 6.3 0.0 0.0 4.6 69.1 SALL1 6299 ENSG00000103449 -2.39 2.66E-03 6.19E-02 126.2 81.2 0.0 112.8 409.7 267.7 SALL2 6297 ENSG00000165821 -4.13 2.94E-05 1.71E-03 72.9 38.6 16.5 11.6 194.2 581.9 SCN11A 11280 ENSG00000168356 -Inf 3.20E-03 7.17E-02 0.0 0.0 0.0 0.0 0.0 43.4 SCN1B 6324 ENSG00000105711 4.36 3.42E-06 2.87E-04 654.7 1438.9 141.0 25.4 31.9 20.2 SCN5A 6331 ENSG00000183873 -Inf 4.18E-03 8.84E-02 0.0 0.0 0.0 0.0 0.0 40.4 SDC2 6383 ENSG00000169439 -3.28 7.59E-04 2.37E-02 18.2 11.0 14.3 47.7 253.9 216.2 SDK2 54549 ENSG00000069188 -3.29 3.28E-03 7.27E-02 44.4 23.9 0.0 4.1 0.0 178.5 SELENBP1 8991 ENSG00000143416 -3.91 7.83E-04 2.42E-02 25.5 5.2 20.1 6.7 110.1 203.2 SEMA3D 223117 ENSG00000153993 -6.30 5.75E-04 1.94E-02 0.0 2.3 0.0 0.0 0.0 82.0 SEMA4G 57715 ENSG00000095539 -3.43 4.43E-03 9.22E-02 29.7 13.2 4.0 0.0 69.2 47.4 SEMA6A 57556 ENSG00000092421 -3.48 6.56E-05 3.32E-03 68.1 50.0 3.1 0.0 257.1 140.0 SERPINE2 5270 ENSG00000135919 3.55 1.21E-04 5.51E-03 1392.0 2436.4 127.5 513.6 92.8 83.1 SEZ6L 23544 ENSG00000100095 6.22 1.07E-03 3.15E-02 103.7 109.6 0.0 4.0 0.0 1.0 SFRP1 6422 ENSG00000104332 -2.10 7.59E-04 2.37E-02 91.7 535.5 0.0 12.3 1178.7 396.2 SFTA3 253970 ENSG00000229415 -Inf 9.82E-07 9.73E-05 0.0 0.0 0.0 0.0 125.0 32.3 SGCD 6444 ENSG00000170624 4.73 1.20E-05 8.39E-04 172.6 443.4 0.0 0.0 0.0 11.0 SH3BGR 6450 ENSG00000185437 3.88 4.80E-06 3.79E-04 47.5 40.0 989.7 672.0 39.6 37.6 SHC4 399694 ENSG00000185634 2.94 4.92E-03 9.93E-02 50.1 30.0 184.2 63.3 12.9 11.1 SHISA2 387914 ENSG00000180730 -Inf 1.15E-03 3.31E-02 0.0 0.0 0.0 0.0 0.0 55.9 SHOX2 6474 ENSG00000168779 Inf 8.30E-04 2.54E-02 41.9 23.4 64.0 0.0 0.0 0.0 SHROOM3 57619 ENSG00000138771 -3.30 3.19E-04 1.23E-02 95.0 29.6 72.1 132.7 807.8 726.4 SIX3 6496 ENSG00000138083 -5.50 1.88E-08 2.91E-06 2.7 26.1 0.0 0.0 203.9 594.6 SIX6 4990 ENSG00000184302 -10.35 4.28E-15 3.74E-12 1.4 1.6 0.0 0.0 1346.6 17.9 SKAP2 8935 ENSG00000005020 4.09 4.19E-05 2.28E-03 52.5 58.8 26.6 360.6 8.4 8.9 SLC15A2 6565 ENSG00000163406 -6.36 1.23E-05 8.53E-04 1.4 1.2 1.9 0.0 150.4 38.3 SLC16A3 9123 ENSG00000141526 Inf 1.99E-03 5.01E-02 0.0 0.0 21.9 52.7 0.0 0.0 SLC26A2 1836 ENSG00000155850 2.94 2.54E-03 5.96E-02 590.4 1552.1 12.7 95.7 96.6 48.5 SLC2A5 6518 ENSG00000142583 Inf 7.62E-05 3.75E-03 1.7 3.1 4.5 109.7 0.0 0.0 SLC38A1 81539 ENSG00000111371 3.22 3.45E-04 1.32E-02 150.8 124.7 320.3 98.7 14.5 24.5 SLC38A5 92745 ENSG00000017483 Inf 8.90E-04 2.70E-02 63.4 20.6 61.7 4.0 0.0 0.0 SLC46A1 113235 ENSG00000076351 Inf 3.44E-03 7.54E-02 12.1 25.0 10.0 34.8 0.0 0.0 SLC4A11 83959 ENSG00000088836 Inf 1.75E-05 1.14E-03 15.5 41.5 87.7 11.6 0.0 0.0 SLC4A4 8671 ENSG00000080493 -4.49 5.85E-07 6.12E-05 36.0 38.9 13.1 18.8 925.2 145.3 SLCO1C1 53919 ENSG00000139155 -Inf 3.19E-09 5.86E-07 7.7 0.0 0.0 0.0 166.2 151.8 SLCO2A1 6578 ENSG00000174640 -5.61 7.54E-08 1.00E-05 38.8 15.5 0.0 0.0 213.0 297.0 SLITRK5 26050 ENSG00000165300 -4.56 7.21E-04 2.29E-02 13.7 0.0 16.3 0.0 46.4 207.6 SMAGP 57228 ENSG00000170545 3.32 4.27E-04 1.58E-02 17.6 11.6 176.0 226.3 8.5 19.2 SMOC2 64094 ENSG00000112562 -Inf 2.12E-04 8.75E-03 2.7 0.0 0.0 0.0 0.0 79.9 SNAP25 6616 ENSG00000132639 3.34 1.14E-04 5.26E-03 306.2 396.7 79.9 513.8 20.5 44.6 SNCAIP 9627 ENSG00000064692 -5.66 3.64E-03 7.90E-02 4.4 1.6 0.0 0.0 2.8 49.4 SNHG12 85028 ENSG00000197989 2.75 1.36E-03 3.77E-02 29.7 29.7 357.1 235.4 25.1 36.6 246
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 SNX10 29887 ENSG00000086300 4.39 2.53E-03 5.95E-02 82.6 39.4 24.4 63.7 0.0 4.3 SNX22 79856 ENSG00000157734 7.52 1.08E-06 1.05E-04 162.4 276.1 1.9 0.0 0.0 1.0 SOD2 6648 ENSG00000112096 3.20 1.06E-04 4.94E-03 45.8 51.4 187.6 1755.6 53.2 90.9 SOD3 6649 ENSG00000109610 Inf 1.66E-10 4.05E-08 112.8 3.1 401.2 0.8 0.0 0.0 SORCS2 57537 ENSG00000184985 -9.04 6.02E-13 2.49E-10 1.5 1.6 0.6 0.0 690.7 77.4 SORCS3 22986 ENSG00000156395 Inf 1.63E-04 7.07E-03 82.4 81.1 2.6 30.0 0.0 0.0 SORL1 6653 ENSG00000137642 3.93 3.16E-04 1.22E-02 586.9 293.8 1.4 52.7 3.0 12.1 SOX10 6663 ENSG00000100146 Inf 1.63E-17 4.85E-14 2350.8 3216.5 0.0 0.0 0.0 0.0 SOX3 6658 ENSG00000134595 3.74 1.67E-04 7.18E-03 2.5 3.1 256.8 75.8 1.8 15.2 SPAG4 6676 ENSG00000061656 5.25 1.07E-03 3.15E-02 6.8 4.7 81.5 30.5 0.0 2.4 SPARCL1 8404 ENSG00000152583 -4.03 2.40E-05 1.48E-03 44.2 39.0 4.8 282.9 1448.1 2097.6 SPINK2 6691 ENSG00000128040 Inf 9.14E-04 2.76E-02 0.0 3.8 79.9 0.0 0.0 0.0 SPINT1 6692 ENSG00000166145 4.31 1.01E-06 9.90E-05 0.0 0.0 1009.1 7.2 19.9 13.7 SPP1 6696 ENSG00000118785 3.58 1.10E-04 5.10E-03 75.6 194.5 2549.4 7850.3 335.4 254.9 SPRED1 161742 ENSG00000166068 -3.32 6.80E-04 2.20E-02 15.4 17.7 6.9 24.1 217.2 101.8 SPTBN5 51332 ENSG00000137877 -5.93 3.39E-05 1.90E-03 0.0 0.0 5.0 0.0 151.8 52.0 SQRDL 58472 ENSG00000137767 3.58 1.07E-03 3.15E-02 31.7 90.8 183.0 52.3 18.4 0.0 SRGAP3 9901 ENSG00000196220 -3.35 5.76E-04 1.94E-02 21.5 14.4 0.0 38.0 214.2 138.7 SRP9 6726 ENSG00000143742 -2.29 2.21E-03 5.38E-02 443.5 726.1 195.4 161.4 1982.7 1557.9 SRPX 8406 ENSG00000101955 2.86 1.23E-03 3.49E-02 1070.0 1473.9 771.8 4757.1 321.8 319.2 ST6GAL1 6480 ENSG00000073849 4.93 4.81E-04 1.71E-02 184.6 171.7 0.7 12.0 0.0 4.0 ST6GALNAC3 256435 ENSG00000184005 -4.73 1.69E-03 4.46E-02 0.0 4.7 0.0 0.0 23.6 59.7 ST6GALNAC5 81849 ENSG00000117069 -8.25 1.01E-11 3.42E-09 8.9 0.0 0.0 5.8 261.3 899.5 STAMBPL1 57559 ENSG00000138134 3.81 7.34E-05 3.66E-03 0.0 0.0 86.7 334.9 3.5 15.9 STC2 8614 ENSG00000113739 3.31 1.18E-03 3.37E-02 0.0 0.0 230.2 26.8 0.0 17.2 STEAP1 26872 ENSG00000164647 6.19 2.40E-07 2.87E-05 6.2 35.9 219.6 104.7 2.5 1.4 STEAP2 261729 ENSG00000157214 3.94 2.25E-05 1.40E-03 0.0 0.0 319.9 414.3 25.9 6.1 STRA6 64220 ENSG00000137868 -5.09 6.26E-07 6.51E-05 0.0 38.8 7.5 9.8 16.7 1255.8 STX3 6809 ENSG00000166900 Inf 5.56E-04 1.88E-02 4.1 0.0 72.6 19.5 0.0 0.0 STXBP5L 9515 ENSG00000145087 -Inf 1.60E-05 1.05E-03 0.0 0.0 0.0 0.0 103.4 0.0 SULF1 23213 ENSG00000137573 -3.79 3.40E-03 7.47E-02 0.0 11.3 0.0 0.0 13.7 86.9 SULF2 55959 ENSG00000196562 3.31 1.15E-04 5.28E-03 749.0 891.0 253.5 581.6 43.3 72.4 SYNGR1 9145 ENSG00000100321 2.48 2.40E-03 5.73E-02 127.2 130.6 487.6 414.2 52.8 71.1 SYNM 23336 ENSG00000182253 -4.23 6.56E-05 3.32E-03 1.4 0.0 0.0 36.4 238.8 212.8 SYT1 6857 ENSG00000067715 -2.46 6.89E-04 2.22E-02 87.5 110.3 0.0 16.1 374.6 93.7 SYTL4 94121 ENSG00000102362 3.14 2.93E-03 6.67E-02 37.0 54.7 71.1 142.0 5.9 14.1 SYTL5 94122 ENSG00000147041 3.34 1.88E-03 4.82E-02 0.0 0.0 14.8 277.9 12.2 7.3 TAGLN 6876 ENSG00000149591 -7.06 8.97E-14 4.44E-11 1.9 3.1 9.4 4.1 1089.6 384.4 TAPBPL 55080 ENSG00000139192 2.57 3.86E-03 8.32E-02 123.3 118.8 114.3 780.6 93.5 20.3 TBC1D8 11138 ENSG00000204634 5.89 5.01E-05 2.62E-03 13.8 15.7 73.7 90.9 0.0 2.4 TCEAL2 140597 ENSG00000184905 Inf 2.51E-08 3.69E-06 1.4 3.3 27.2 248.9 0.0 0.0 TCF7 6932 ENSG00000081059 3.00 6.69E-04 2.18E-02 59.5 70.8 87.7 368.1 8.4 35.1 TCF7L2 6934 ENSG00000148737 -2.60 3.98E-03 8.49E-02 33.8 34.3 69.4 42.3 343.9 248.4 TECRL 253017 ENSG00000205678 Inf 3.34E-06 2.83E-04 256.3 195.2 0.0 0.0 0.0 0.0 TES 26136 ENSG00000135269 -Inf 6.77E-12 2.45E-09 0.0 0.0 0.0 0.0 433.0 184.2 TESC 54997 ENSG00000088992 -3.42 2.19E-03 5.38E-02 21.6 13.6 0.0 0.0 92.8 8.6 TF 7018 ENSG00000091513 3.70 4.33E-03 9.07E-02 140.3 205.9 0.0 14.5 5.5 6.1 TFAP2A 7020 ENSG00000137203 3.71 4.55E-04 1.64E-02 476.7 357.8 42.5 104.2 26.0 0.0 TFCP2 7024 ENSG00000135457 5.47 6.46E-04 2.12E-02 47.7 99.6 20.3 14.7 0.0 2.0 TGFA 7039 ENSG00000163235 4.55 3.44E-05 1.92E-03 216.7 272.7 99.7 54.3 12.1 0.0 TGM2 7052 ENSG00000198959 3.93 9.46E-06 6.83E-04 0.0 62.7 290.3 418.6 11.5 22.5 THBS2 7058 ENSG00000186340 3.55 2.42E-05 1.48E-03 237.0 73.4 39.0 1655.3 38.9 61.5 247
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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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E. Exon Array Data Appendix Average
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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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