Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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A.3 Quantitative RT-PCR Appendix Well Applied Biosystems assay ID Gene G19 G19 G21 G21 G23 G23 G24 G24 G25 G25 G26 G26 G30 G30 G31 G31 G32 G32 G144 G144 G166 G166 G179 G179 Category A B A B A B A B A B A B A B A B A B A B A B A B 51 MAP6-Hs01929835_s1 Core down 26.0 26.1 25.9 25.7 29.1 30.2 30.2 28.3 29.2 30.7 32.0 31.6 27.3 27.6 30.6 30.4 29.1 30.7 32.2 29.8 31.9 34.0 26.6 26.3 52 PDE1C-Hs01095694_m1 Core up 24.8 25.0 28.2 28.9 25.2 24.2 24.1 23.3 24.1 24.0 26.1 25.5 26.9 26.5 28.9 28.5 28.7 28.5 25.0 25.2 23.9 23.6 25.5 25.5 53 SULF2-Hs00378697_m1 Core up 23.9 24.3 27.0 26.1 24.3 26.4 23.1 22.0 24.3 24.1 24.3 25.4 23.5 23.2 25.9 25.0 25.7 25.8 25.0 23.5 26.2 25.5 26.0 26.0 54 TUBB-Hs00962420_g1 Norm 20.7 21.3 20.9 20.9 21.5 21.4 21.4 21.3 21.5 21.2 21.5 21.8 21.1 21.2 20.7 20.6 20.6 20.5 21.2 21.2 20.7 20.1 22.5 22.7 55 LMO2-Hs00277106_m1 Core down 30.6 30.1 27.2 26.2 31.3 35.6 31.3 29.9 34.0 34.4 27.9 30.2 26.3 27.4 26.9 26.5 26.6 26.1 30.0 31.4 34.3 35.6 29.0 28.9 56 MAN1C1-Hs00220595_m1 Core up 27.9 26.9 25.8 25.2 32.1 34.2 29.7 28.8 26.9 26.7 24.8 25.9 25.6 25.9 25.8 24.9 26.0 25.5 26.3 26.3 28.1 27.4 26.2 26.6 57 TAGLN-Hs00162558_m1 Core down 28.4 29.7 37.9 33.3 24.9 27.3 21.4 21.1 26.2 25.4 29.7 29.0 26.1 25.0 33.7 31.0 29.3 29.4 27.4 30.2 31.4 29.8 26.9 26.7 58 RTN1-Hs00382515_m1 Core down 25.1 24.8 33.6 32.9 27.8 28.8 29.8 28.7 32.2 32.3 25.5 26.2 25.8 25.8 28.9 27.7 29.8 30.3 27.0 28.1 29.1 30.8 30.8 30.6 59 MAF-Hs00193519_m1 Core down 28.2 27.5 28.7 28.9 27.5 30.2 28.5 28.3 31.1 31.9 27.3 28.4 27.8 28.0 27.8 28.0 28.4 27.5 31.4 32.1 28.1 28.7 34.7 34.5 60 NPTX2-Hs00383983_m1 Core down 30.1 27.8 29.0 32.2 28.9 29.3 34.5 36.6 36.7 35.0 27.8 26.5 32.3 31.8 31.2 29.3 34.2 30.2 31.7 32.1 28.4 29.3 31.8 32.3 61 EDA2R-Hs00939736_m1 Core down 27.5 27.4 28.8 28.6 29.2 26.9 28.4 27.8 35.2 35.2 32.7 32.2 28.8 28.8 35.4 35.0 30.6 32.2 34.4 32.8 32.0 30.2 34.6 34.3 62 SOX10-Hs00366918_m1 Marker 37.3 36.6 37.9 37.3 37.3 37.1 37.0 36.6 24.4 25.2 37.6 36.7 35.4 35.6 37.9 37.6 37.8 37.7 24.5 24.5 38.0 37.1 36.2 36.9 63 SEMA6A-Hs00221174_m1 Core down 26.9 25.9 23.3 23.6 25.9 26.2 24.1 24.5 27.4 27.6 25.2 26.4 24.3 24.4 23.4 23.4 23.6 23.7 24.7 25.0 26.3 27.2 27.2 27.6 64 DDIT3-Hs00358796_g1 Core up 27.0 26.8 28.0 28.1 25.2 22.4 27.6 26.8 26.8 26.3 28.3 28.7 27.3 27.2 22.0 21.7 21.8 21.8 22.5 23.2 25.3 23.8 26.4 25.9 65 CA12-Hs01080909_m1 Core down 30.4 28.1 23.3 23.6 25.8 26.6 31.8 30.0 27.6 27.3 24.1 25.9 27.1 28.4 24.8 24.4 24.8 23.9 25.8 25.1 26.9 26.9 25.6 25.9 66 C9orf125-Hs00260558_m1 Core down 31.0 31.1 37.9 37.3 34.8 37.1 29.1 28.5 31.8 32.3 30.4 31.3 27.3 27.9 37.9 37.6 37.3 37.3 29.4 29.2 32.3 34.1 35.1 34.8 67 SDC2-Hs00299807_m1 Core down 26.3 26.5 36.0 36.3 26.2 26.4 25.6 25.2 25.6 25.3 26.4 26.3 29.4 29.2 29.0 28.2 29.6 29.6 26.7 27.8 27.9 28.6 25.4 25.3 68 SLIT2-Hs00191193_m1 Core down 25.4 23.8 34.2 32.3 26.2 26.3 32.8 30.6 33.5 32.7 32.3 31.8 33.7 34.8 29.8 29.6 27.6 27.9 30.4 32.1 33.1 33.5 30.7 30.6 69 MT2A-Hs02379661_g1 Core up 22.9 22.6 22.6 21.8 21.2 22.0 23.3 22.7 23.7 22.9 20.6 21.5 22.2 22.7 22.3 22.0 22.1 22.4 21.8 21.7 19.8 18.6 19.2 18.8 70 IL17RD-Hs00296982_m1 Core down 26.6 26.5 26.4 26.9 24.0 24.5 26.8 26.6 27.7 27.4 27.2 28.2 26.5 26.6 27.1 27.0 26.9 27.4 26.4 26.6 29.0 28.2 27.2 27.5 71 PDZRN3-Hs00392900_m1 Core down 29.3 27.9 27.3 27.0 34.2 37.1 36.2 36.6 26.4 26.4 28.3 28.3 29.0 29.5 27.3 26.9 26.9 26.7 30.5 31.7 31.8 31.8 28.2 28.9 72 LGALS3-Hs00173587_m1 Core up 25.1 24.3 25.2 25.0 23.4 23.4 27.1 25.2 24.4 25.0 23.1 23.8 24.7 24.9 26.3 25.4 25.1 25.3 25.2 24.8 25.1 23.2 23.8 23.2 73 FAM69A-Hs00961685_m1 Core up 25.3 24.4 24.6 25.6 25.1 27.8 25.7 23.6 25.4 25.9 24.9 25.6 26.8 26.9 26.1 26.0 25.7 25.8 25.6 25.3 27.1 26.1 26.6 25.9 74 TERT-Hs00972656_m1 Marker 31.8 32.5 29.0 27.2 30.7 30.3 31.9 31.3 31.0 30.8 31.2 31.7 30.2 29.9 30.7 30.2 30.3 29.9 29.4 28.2 30.2 29.9 33.9 34.7 75 PLS3-Hs00418605_g1 Core up 21.9 22.3 25.3 25.8 23.1 23.1 22.1 22.4 23.9 23.7 23.1 23.6 25.3 25.1 25.3 25.4 25.6 25.0 24.0 23.4 22.1 22.5 25.5 24.9 76 PTEN-Hs02621230_s1 Core down 29.2 29.2 33.8 30.6 28.1 28.7 29.1 28.5 29.6 30.3 31.0 31.1 28.5 28.7 31.3 31.5 31.1 31.4 34.5 35.8 30.1 31.2 36.2 34.8 77 SALL2-Hs00826674_m1 Core down 34.2 32.2 32.6 33.4 33.8 37.1 33.9 32.1 32.8 33.1 33.5 34.2 32.8 32.4 32.0 32.1 31.8 31.8 32.8 33.4 33.4 31.9 30.6 30.7 78 KCTD12-Hs00540818_s1 Core down 32.2 31.6 30.4 32.3 30.4 31.9 26.3 25.9 27.6 28.5 28.9 29.0 28.0 28.2 30.9 31.7 30.2 31.5 28.3 29.8 30.4 30.1 25.9 26.5 79 TES-Hs00210319_m1 Core down 37.3 36.6 37.9 37.3 34.5 36.6 34.5 36.4 33.8 34.6 37.6 36.7 37.4 37.6 37.9 37.6 37.8 37.7 34.5 35.8 37.2 36.2 35.0 33.3 80 SOX2-Hs01053049_s1 Marker 24.0 23.5 22.9 23.0 24.8 24.6 24.6 24.4 23.2 23.9 23.4 24.5 23.0 23.2 23.2 23.0 22.8 23.3 23.4 23.9 25.5 27.0 21.9 21.8 81 LPAR6-Hs00271758_s1 Core down 29.9 29.5 29.7 29.7 30.0 31.4 29.2 28.7 33.0 33.2 31.1 31.9 28.6 28.6 29.9 29.3 29.8 29.4 31.6 31.7 29.8 30.3 31.3 31.2 82 ODZ2-Hs00393060_m1 Core down 25.9 26.0 27.6 28.9 25.0 26.1 28.6 26.5 31.6 31.4 25.5 26.5 31.0 31.0 28.0 26.9 28.7 27.9 27.1 28.2 31.0 32.3 27.2 27.4 83 NNMT-Hs00196287_m1 Core up 28.3 27.9 30.9 30.9 24.1 27.2 33.2 29.9 27.9 27.3 24.3 24.2 27.6 27.8 29.9 28.7 30.6 29.0 25.0 26.8 24.0 24.1 23.5 23.4 84 CACNG8-Hs01100182_m1 Core down 32.0 30.5 28.1 28.9 30.4 29.9 31.0 36.6 33.3 33.3 34.3 34.0 27.3 27.6 31.8 33.2 30.4 30.7 27.7 27.7 31.4 31.9 32.0 33.3 85 PRSS12-Hs00186221_m1 Core up 24.5 25.3 31.2 33.8 25.1 24.6 31.5 31.5 27.4 27.0 25.9 26.6 37.4 37.6 28.4 28.3 27.7 27.5 24.8 24.6 24.3 24.4 30.7 31.1 86 FOXJ1-Hs00230964_m1 Core down 32.8 30.1 31.8 31.2 33.8 36.5 31.1 30.5 29.9 31.2 30.3 30.9 28.2 28.3 31.4 31.3 30.6 31.2 30.3 30.9 36.2 37.1 31.1 31.8 87 NTN1-Hs00180355_m1 Core down 29.5 28.5 27.5 26.6 34.5 35.7 25.9 24.6 27.7 28.4 28.7 30.2 27.4 27.4 26.4 26.5 26.5 26.3 25.5 26.8 31.5 35.1 28.6 29.8 88 LMO3-Hs00375237_m1 Core down 37.3 36.6 33.0 35.2 31.9 33.7 37.5 36.6 36.7 37.4 28.7 28.6 32.4 31.2 28.0 28.5 28.2 29.3 34.5 35.8 38.0 37.1 35.1 34.2 89 CHI3L1-Hs00609691_m1 Marker 31.6 25.5 30.7 28.1 33.4 37.1 24.8 23.7 29.0 31.1 24.4 27.1 22.1 23.4 28.5 28.2 29.0 29.9 34.5 35.8 24.0 28.4 21.5 21.7 90 CD9-Hs01124025_g1 Core up 23.4 23.6 23.3 23.9 24.7 24.4 26.0 24.6 22.1 22.9 23.5 24.2 22.8 23.0 23.5 23.5 23.4 23.8 22.6 22.7 23.4 23.2 23.4 22.9 91 ADD2-Hs00242289_m1 Core up 26.8 27.3 24.9 25.5 26.8 25.3 27.2 27.4 28.3 28.3 30.9 31.7 26.2 26.5 25.8 25.5 25.6 25.6 26.4 26.5 26.6 25.5 28.2 28.7 92 MYL9-Hs00697086_m1 Core down 33.0 32.5 32.3 31.6 27.6 29.8 23.3 22.9 28.3 28.1 26.8 27.6 28.7 27.9 34.7 32.8 31.1 31.5 30.5 31.6 26.7 26.2 26.6 26.8 93 LYST-Hs00179814_m1 Core up 30.1 29.8 30.7 31.0 29.9 28.5 29.7 28.6 28.6 29.6 29.9 31.3 28.7 29.3 29.8 29.8 29.9 30.6 27.6 28.2 29.1 28.1 28.1 27.7 94 LAMA2-Hs00166308_m1 Core down 30.2 28.9 37.8 37.3 28.8 29.9 37.5 35.6 31.2 33.4 32.8 32.2 31.0 31.8 30.5 29.4 36.0 35.4 26.8 27.0 33.7 34.1 33.2 34.9 95 PLA2G4A-Hs00233352_m1 Core up 28.4 28.7 30.2 29.3 29.6 29.5 30.6 29.4 26.8 27.4 31.8 31.8 26.9 26.7 27.4 26.8 27.1 26.8 26.5 27.2 29.6 27.5 29.0 28.7 96 BACE2-Hs00273238_m1 Core up 25.1 25.2 35.6 37.3 29.7 30.5 26.9 26.1 25.7 25.9 27.2 28.9 27.8 28.3 30.8 30.4 30.3 30.8 26.3 26.3 26.8 25.7 27.0 26.9 264
A.4 Tag-seq vs qRT-PCR Correlation Appendix A.4 Tag-seq vs qRT-PCR Correlation The correlation between the qRT-PCR measurements from the 21 cell lines (16 GNS and 5 NS cell lines) and the Tag-seq measurements from the five cell lines (three GNS and two NS cell lines) was found by taking the normalised Ct values and tag counts for each <strong>of</strong> the 82 core differentially expressed genes - as determined by Tag-seq on the three GNS cell lines and two NS cell lines - and applying the cor function from the stats R package. Table A.5: Pearson correlation values between the normalised Ct values measured through qRT-PCR and the tag counts measured across the five GNS and NS cell lines assayed via Tag-seq. Gene name Pearson Gene name Pearson correlation correlation PTEN 0.9973 MAN1C1 0.9953 NDN 0.9942 HMGA2 0.9932 HOXD10 0.9925 TUSC3 0.9888 TES 0.9848 SYNM 0.9823 SIX3 0.9800 LYST 0.9797 MYL9 0.9777 PLA2G4A 0.9757 IRX2 0.9749 DDIT3 0.9748 MT2A 0.9741 MMP17 0.9735 BACE2 0.9684 MAF 0.9672 CA12 0.9653 LMO3 0.9652 NKX2-1 0.9625 IL17RD 0.9571 SEMA6A 0.9560 CXXC4 0.9520 FAM69A 0.9475 ADD2 0.9451 SPARCL1 0.9416 LMO2 0.9391 CHCHD10 0.9388 PLCH1 0.9362 PEG3 0.9345 CCND2 0.9344 KALRN 0.9310 FAM38B 0.9278 EDA2R 0.9270 GPR158 0.9222 LMO4 0.9203 CD9 0.9187 ODZ2 0.9168 ST6GALNAC5 0.9139 MAP6 0.9116 NPTX2 0.9047 CACNG8 0.9045 SLIT2 0.9016 MMRN1 0.8906 CD74 0.8906 TAGLN 0.8874 PDE1C 0.8832 CEBPB 0.8813 DNER 0.8811 FUT8 0.8804 C9orf125 0.8772 RAB6B 0.8709 PI15 0.8654 NTN1 0.8620 SULF2 0.8602 KCTD12 0.8384 PMEPA1 0.8322 LUM 0.8263 SALL2 0.8078 NNMT 0.8034 HLA-DRA 0.7884 RTN1 0.7777 MN1 0.7714 RGS5 0.7679 CTSC 0.7661 C5orf13 0.7595 PLS3 0.7439 NELL2 0.7146 NTRK2 0.7115 LPAR6 0.7090 EPDR1 0.7053 LAMA2 0.6889 SDC2 0.6595 S100A6 0.6580 FOXG1 0.6051 PDZRN3 0.6032 FBLN2 0.5795 PRSS12 0.5211 LGALS3 0.5204 DTX4 0.4964 FOXJ1 0.4454 265
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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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