Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 110 for “"TCGA"”.
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Integrative Analysis of Omics Data In Adult Glioma and Other Tcga Cancers to Guide Precision Medicine
… panel of novel fusion transcripts across all of TCGA cancer types through transcriptomic profiling. Then I have predicted fusion proteins with kinase activity and hub function of pathway network based on the annotation of genetically mobile domains and functional domain architectures. I have …
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Systemic analysis of changes in protein modification and gene coexpression networks in cancer
… a large scale, disease-associated mutations from TCGA, Uniprot, and dbSNP were integrated with PTM sites from PhosphoSitePlus. We characterized each dataset individually, compared somatic with germline mutations, and analyzed PTM sites intersecting directly with disease variants. To assess the …
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Exploring topological data analysis in gene expression data topology-driven biomarker discovery and clinical outcome prediction in oncology
… three classification tasks: cancer type (using TCGA-SARC, TCGA-PCPG, and TCGA-ESCA datasets), cancer staging (using TCGA-HNSC for stages I–IV), and treatment response (responders vs. non-responders). For biomarker identification, the same three tasks were applied using the best performing …
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Haplotype-Informed Allelic Imbalance Detection From Rna In Cancer
… samples from 7 sites in The Cancer Genome Atlas (TCGA), inferring genotypes directly from RNA-sequencing (RNA-seq). This resulted in an SCNA detection rate of 68%. Encouraged by this, we next leveraged large public genetic reference data and array derived germline genotypes, from matched blood …
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Identification of epigenetically dysregulated genes in tumours that metastasise to the brain
… breast tumours from The Cancer Genome Atlas (TCGA) and Genome-wide methylation analysis of metastatic brain tumors that originated from primary breast tumours were carried out. A candidate gene approach identified two genes (BNC1 and CCDC8) dysregulated in breast to brain metastases (BBM) from …
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IDENTIFYING EARLY STEPS IN THE DEVELOPMENT OF HBV ASSOCIATED HCC
… data originally from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project were used to compare truly healthy liver tissues, a base-line level often excluded from cancer studies, to both non-tumor and tumor tissues of patients with HBV associated HCC. This illuminated …
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Characterization of The Growth Factor Receptor Network Oncogenes in Lung Cancer
… tumors acquired from The Cancer Genome Atlas (TCGA). Each gene signature underwent validation using proteomics data from The Cancer Proteome Atlas (TCPA) and gene expression. Following thorough analysis, optimal gene signatures were determined for the genes BAD, HER2, IGF1R, RAF, and KRAS. In …
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DawnRank: discovering personalized driver genes in cancer
… genes on a single patient level. Applications to TCGA datasets demonstrated the effectiveness of our method. We believe DawnRank complements existing driver identification methods and will help us discover personalized causal mutations that would otherwise be obscured by tumour heterogeneity.
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The Immune Microenvironment of Microsatellite Instable Endometrial Cancer
… cancer data from The Cancer Genome Atlas (TCGA) was used to study immune-related gene expression in MSI-H EC compared to MSS EC at both the individual gene and pathway level. Fluorescent multiplexing immunohistochemistry (IHC) was used to evaluate differences in immune cell populations …
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A Method for Identification of Pancreatic Cancer through Methylation Signatures in Cell-Free DNA
… available data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). The work includes the development of methods for simulation of samples and cell-free DNA data at multiple ctDNA concentrations as well as a pilot implementation and evaluation of a machine learning model …
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Investigating the utility of blood borne oncological biomarkers in solid tumours: glioma and melanoma
… samples and the human cancer genome atlas (TCGA) glioma derived RNA profile. Moreover, this research work explored the relationship between plasma cell-free DNA (cfDNA), serum lactate dehydrogenase (LDH), plasma vascular endothelial growth factor (VEGF), programmed death ligand-1 (PD-L1), …
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Integration of Multi-Platform High-Dimensional Omic Data
… and survival using The Cancer Genome Atlas (TCGA) datasets. The simulation studies demonstrate the superior performance of SIFORM in terms of biomarker detection accuracy. In lung cancer applications, SIFORM identifies many biomarkers that belong to key pathways for lung tumorigenesis. It …
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Cell-free DNA and tumor exosome cargo as diagnostic and prognostic marker for prostate cancer
… We performed differential expression (DE) of TCGA data and exosomal miRNA data and which we identified 185 miRNA and 65 miRNAs respectively. A comparison of the differential expressed TCGA miRNA and exosomal miRNA showed 13 miRNAs common between the two data with 7 of the 13 miRNAs expressed …
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The impact of the Human papillomavirus type 16 on non-coding RNAs in Head and Neck cancer
… having a downstream impact on miR-496. TCGA analysis showed that SREBF2 was significantly higher in the HPV+ OPC. An siRNA knockout of HPV16 E6/E7 revealed that the viral oncogenes could regulate SREBF2 and miR-33a. The knockdown of SREBF2, revealed no change in miR-33a expression, …
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Segregation similarity loss in morphological ranking of image search in histopathology
… three-tumor-type brain, lung, and kidney from TCGA repository. The results show that the proposed model, compared to state-of-the-art models, i.e., KimiaNet, can classify cancer subtypes more accurately and provides superior results. Besides, the proposed model achieves memory and computational …
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Developing Bottom-Up, Integrated Omics Methodologies for Big Data Biomarker Discovery
… in disease states. The Cancer Genome Atlas (TCGA) provides high-dimensional patient data and illustrates the trends that occur in expression profiles and their alteration in many complex disease states. I will ultimately create a bottom-up multi-omics approach to observe biological systems …
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Impact of the gut microbiota on DNA methylation in colorectal cancer
… and CIMP by analyzing the Cancer Genome Atlas (TCGA) 450K methylation array data and whole exome sequencing data. The analysis demonstrated that bacterial Superhigh cases in the TCGA datasets also had significantly higher odds of being CIMP-Positive and having MLH1 methylation. To expand our …
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Novel Network-Based Models for High-dimensional Data
… sequencing data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Project (GTEx) to predict breast cancer occur rence, severity, and recurrence. Our analysis identified novel breast cancer risk genes, including ADCY4, COL1A1, and FGF4, and resulted in improved prediction …
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Identification of Circulating MicroRNAs as Biomarkers in Glioblastoma
… GBM tissue data from The Cancer Genome Atlas (TCGA) identified potential differences in origin of the four miRNA biomarkers; miR-20a-5p in the serum of GBM patients was likely to originate from the GBM. MiR-34a-5p showed increased expression in the GBM tissue analysed by TCGA. In contrast, …
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Igfbp2 Potentiates Egfr-Stat3 Signaling In Glioma
… and STAT3-activated genes derived from the TCGA database for human glioma. A high level of all 3 proteins (IGFBP2, EGFR and STAT3) was strongly correlated with poorer survival in an independent patient dataset. These results identify a novel tumor-promoting function for IGFBP2 of activating …
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