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 48 for “"Gene set enrichment analysis"”.
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Using co-expression to redefine functional gene sets for gene set enrichment analysis
Manually curated gene sets related to a biological function often contain genes that are not tightly co-regulated transcriptionally. which obscures the evidence of coordinated differential expression of these gene sets in relevant experiments. To address this problem, we explored strategies to …
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Pareto Task Inference Analysis of Single-Cell RNASequencing of Human Placenta Reveals Biological Insightsinto Adverse Pregnancy Outcomes
… clustering. However, these techniques may generate limited representations of nuanced cellular functions and biological relationships among and within cell clusters. Pareto Task Inference (ParTI), a dimensionality reduction technique that fits data to an n-dimensional polygon or polytope, …
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Gene Set Anomaly Score: A Genomic Data and Knowledge Driven Approach for Analysing Anomalous Gene Expression in Cancer Patients
Genomics research often uses Gene Set Enrichment Analysis (GSEA) to rank genes that correlate with the presence of phenotypical traits and to interpret how variations in gene expression influence those traits. GSEA provides an explanation of found genes through their associations with gene sets. As …
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A histopathological and genomics study of the mutated human FAM111B gene related POIKTMP disease
… associated with mutations of the human FAM111B gene. FAM111B gene codes for a protein whose function is not well characterized. Therefore, elucidating the mechanism of FAM111B or its mutations in POIKTMP is beneficial to understanding the complexities surrounding this multisystemic fibrosing …
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A histopathological and genomics study of the mutated human FAM111B gene related POIKTMP disease
… associated with mutations of the human FAM111B gene. FAM111B gene codes for a protein whose function is not well characterized. Therefore, elucidating the mechanism of FAM111B or its mutations in POIKTMP is beneficial to understanding the complexities surrounding this multisystemic fibrosing …
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Statistical methods for gene set based significance analysis.
Gene set enrichment analysis (GSEA) is a method to identify groups of genes, which are statistically more differentially expressed than all other genes across different treatments within a microarray study. Most of the existing approaches have largely relied on nonparametric methods and require …
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Role of ETV5 Mutations in B Cell Acute Lymphoblastic Leukemia
… B-ALL in which leukemia is driven by deletion of genes encoding the ETS transcription factors, PU.1 and Spi-B. Whole exome sequencing was performed on PU.1-/Spi-B null leukemias to identify additional driver mutations and showed that there were frequent mutations in ETS variant transcription …
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Identification of Oncogenic KRAS-Associated Vulnerabilities in Non-Small Cell Lung Cancer
… in KRAS are frequently involved in the pathogenesis of non-small cell lung cancer (NSCLC), the disease responsible for the most cancer-related deaths in the US. Despite intensive efforts to develop drugs that directly interfere with KRAS activity over the past decade, no effective inhibitor …
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Genomic response, bioinformatics, and mechanics of the effects of forces on tissues and wound healing
… Cellular behavioral changes can be traced to gene expression profile changes. These effects were studied in the context of Micromechanical force therapy, a novel therapeutic treatment in the management of different types of wounds. The mechanism of therapies that work by applying suction …
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Transcriptomic Signatures of Skeletal Muscle Adaptation: Disuse, Rehabilitation, and Resistance Exercise Intervention
… Additionally, we used a novel approach to gene set enrichment analysis (GSEA) to determine which biological pathways are associated with improvements in important muscle phenotypes including lean mass and strength. We revealed that pathways associated with mitochondrial function are …
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Arid1a Haploinsufficiency Initiates Neural Crest Transformation in a Mouse Model of Mycn-driven Neuroblastoma
… in the chromatin remodeler and tumor suppressor gene (TSG) ARID1A. Additional causal studies supported ARID1A’s candidacy as a putative 1p36 TSG in MYCN-driven NBL. This study aimed to causally test Arid1a loss during Mycn-driven NBL initiation through the development of a mouse model of high …
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Investigating the genome of Anaplastic Lymphoma Kinase-positive Anaplastic Large Cell Lymphoma
… (WES) of ALK+ ALCL was performed, as well as Gene-Set Enrichment Analysis. This revealed that the Notch pathway was the most enriched in mutations. In particular, variant T349P of Notch1, which confers a growth advantage to cells in which it is expressed, was detected in 12% of ALK+ and ALK- …
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An investigation of the role of TRIB2 in steady state and stressed haematopoiesis
… rise to increased number of mature thymic subsets. During stressed haematopoiesis, Trib2-/- developing thymocytes demonstrate hypersensitivity to 5-fluorouracil-induced cell death. Nevertheless, Trib2-/- mice exhibit accelerated thymopoietic recovery post 5-fluorouracil treatment due to …
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Malignant Gliomas Originate From Neural Stem/Progenitor Cells and Are Maintained By Cancer Stem Cells
… glioma at the molecular level, we have performed gene set enrichment analysis (GSEA) comparing the molecular signature of tumors that develop in our mouse glioma models to the gene expression profiles of a number of human tumors. Our mouse glioma models share high similarity with human GBM and …
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The Transcriptional Profile of Microglia: From Brain to Dish
… and understand how clinical phenotypes influence gene expression? 2. How accurately do current simple in-vitro model systems of human microglia capture the profile of primary human cells? 3. Do more complex model systems move cultured cells further along a trajectory towards the primary cell type? …
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Elucidating age and pregnancy related alterations in the murine mammary gland
Breast cancer is a heterogeneous disease that is the prevailing cause of cancer-related deaths in women. However, many studies have shown that a full-term pregnancy early in life can decrease the chance of developing cancer by up to 50% during menopause [1]. This is one of the highest protective …
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Exploiting gene expression and protein data for predicting remote homology and tissue specificity
… biological data. The importance of such analysis as a means of making inferences about biological functions is widely acknowledged in the bioinformatics community. Specifically, this work makes three novel contributions based on the systematic analysis of publicly archived data of protein …
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A pathways-based approach identifying determinants of drug resistance in oesophageal adenocarcinoma
… Diagnostics Xcel array™. The Broad Institute’s Gene Set Enrichment Analysis (GSEA) software was used to identify pathways enriched between non-responders to chemotherapy and responders, identifying genes differentially regulated between the two groups. A focused siRNA screen of 80 target genes …
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Multi-omics Data Integration for Identifying Disease Specific Biological Pathways
Pathway analysis is an important task for gaining novel insights into the molecular architecture of many complex diseases. With the advancement of new sequencing technologies, a large amount of quantitative gene expression data have been continuously acquired. The springing up omics data sets such …
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The Design and Assembly of 3D Liver Mimetic Cellular Architectures
… period using DNA microarray measurements and Gene Set Enrichment Analysis (GSEA) in order to derive biologically meaningful information at the level of gene sets. The gene expression in CS cultures steadily diverged from that in HMs. Gene sets up-regulated in CS are those linked to liver …
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