Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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List of Abbreviations 5-bromo-2’-deoxyuridine BrdU AGO Argonaute AKT v-akt murine thymoma viral oncogene APC Antigen Presenting Cell ARF Alternate Reading Frame ASR Age Standardized Rate ATM Ataxia telangiectasia mutated BLBP Brain lipid binding protein BMP Bone Morphogenetic Protein Ca 2+ Calcium CCDS Consensus Coding Sequence CD133 Prominin CD144 Vascular endothelial-cadherin CDK Cyclyn-Dependent Kinase CDKN Cyclyn-Dependent Kinase Inhibitor CGH Comparative genomics hybridization CHI3L1 Chitinase 3-like 1 CNA Copy Number Aberrations CNS Central Nervous System CO2 Carbon dioxide CSF Cerebro Spinal Fluid Ct Cycle threshold CTL Cytotoxic Lymphocyte CTMP C-terminal modulator protein CpG Cytosine-phosphate-Guanine DNA Deoxyribonucleic Acid Dcx Doublecortin ECM Extracellular matrix EGF Epidermal Growth Factor EGFR Epidermal Growth Factor Receptor ES Embryonic Stem EST Expressed Sequence Tags FACS Fluorescent Activated Cell Sorting FC Fold change FDR False Discovery Rate FGF2 Fibroblast Growth Factor 2 FGF2 Fibroblast growth factor 2 FISH Fluorescence In Situ Hybridization FOXO Forkhead box O G-CIMP Glioma CpG Island Methylator Phenotype GABA Gamma-aminobutyric acid GBM Glioblastoma Multiforme GEMM Genetically Engineered Mouse Model GFAP Glial Fibrillary Acidic Protein GFAP Glial Fibrillary Acidic Protein GFP Green Fluorescent Protein GLAST Glutamate Aspartate Transporter GO Gene Ontology GSEA Gene Set Enrichment Analysis GTP Guanosine-5’-triphosphate GTPase Guanosine-5’-triphosphate hydrolase HGNC HUGO gene nomenclature committee HIF1 Hypoxia Inducible Factor 1 HIF1A Hypoxia Inducible Factor 1, subunit α ICM Inner Cell Mass IDH1 Isocitrate Dehydrogenase 1 IQGAP1 IQ motif containing GTPase activating protein 1 IRES Internal Ribosome Entry Site KEGG Kyoto Encyclopedia of Genes and Genomes LIF Leukemia Inhibitory Factor 306
Ln Natural logarithm LOH Loss of Heterozygosity MAP2 Microtubule-associated protein 2 MAPK Mitogen Activated Protein Kinase MDM2 Mdm2 p53 binding protein homolog MDM4 Mdm4 p53 binding protein homolog MGC Mammalian Gene Collection MGI Mouse Genome Informatics MGMT O-6-methylguanine-DNA methyltransferase MIQE Minimum Information for publication of Quantitative real-time PCR Experiments MMR Mismatch Repair MSH6 MutS homolog 6 NADPH Nicotinamide Adenine Dinucleotide Phosphate NCBI National Center for Biotechnology Information NEP Neuroepithelial progenitor NF1 Neurofibromin 1 NS Neural Stem OCT4 Octamer-binding protein 4 OLIG2 Oligodendrocyte lineage transcription factor 2 ORF Open Reading Frame PCA Principal Component Analysis PDGF Platelet-Derived Growth Factor PDGFR Platelet-Derived Growth Factor Receptor PDPK1 3-phosphoinositide dependent protein kinase-1 PHLPP PH domain and leucine rich repeat protein phosphatase 1 PI3K Phosphoinositide-3-Kinase PI3KR Phosphoinositide-3-Kinase Receptor PIP3 phosphatidylinositol (3,4,5)-trisphosphate PTEN Phosphatase and tensin homolog Pax6 Paired box gene 6 RA Retinoic Acid RAS Rat Sarcoma RB1 Retinoblastoma 1 RISC RNA Induced Silencing Complex RNA Rybonucleic Acid RTK Receptor Tyrosine Kinase SAGE Serial Analysis of Gene Expression SCV Squared Coefficient of Variation SGZ Subgranular Zone SHH Sonic hedge hog SILAC Stable Isotope Labeling by Amino acids in Cell culture SKY Spectral Karyotyping SNP Single Nucleotide Polymorphism SOX1 Sex determining region Y-box 1 SOX2 Sex determining region Y-box 2 SSEA1 Stage-specific embryonic antigen 1 SVZ Subventricular Zone TCGA The Cancer Genome Atlas TGFβ Tumour Growth Factor β TP53 Tumor Protein 53 TUBB type III β-tubulin Tag-seq Tag sequencing UCSC University California Santa Cruz UTR Untranslated Region VZ Ventricular Zone WHO World Health Organization aCGH array comparative genomics hybridization bp base pair iHOP information Hyperlinked Over Proteins mRNA messenger RNA mm millimeter ncRNAs non-coding RNAs nt nucleotide oligo-dT oligo deoxy-thymine poly-A poly-adenine poly-T poly-thymine qRT-PCR quantitative Real-Time PCR rRNA ribosomal RNA tpm tags per million UCSC University of California Santa Cruz
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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.2 Classified Differential Express
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A.2 Classified Differential Express
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Page 277 and 278: End Select End If End Sub Appendix
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Page 281 and 282: Appendix C Long ncRNAs We detected
Page 283 and 284: C. Long ncRNAs Appendix Tag Accessi
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Page 291 and 292: D.2 Pathway Images Appendix Figure
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Page 295 and 296: E. Exon Array Data Appendix Average
Page 309 and 310: F. MicroRNA Array Data Appendix Tab
Page 311 and 312: F. MicroRNA Array Data Appendix GNS
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Page 323 and 324: Bibliography [1] Cell signaling tec
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