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 22 for “"Gene Set Enrichment Analysis (GSEA)"”.
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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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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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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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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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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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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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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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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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Gene Set Analysis of Post-Lactational Mammary Gland Involution Gene Signatures In Inflammatory and Triple Negative Breast Cancer
… and Stein et al. (2004) conducted a detailed analysis of these changes in the mouse mammary gland. Their results showed that tissue remodeling during post-lactational involution period mimics wound healing and tumorigenesis like pathological conditions. This indicates that post-lactational …
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Identification and characterisation of non-coding RNAs involved in ductal carcinoma in situ
… that, two candidates were selected for in-depth analysis: vtRNA2-1 and MEG3. Their expression was also measured in a small cohort of DCIS patients (n=12) and the overexpression observed in cell lines was confirmed. Vault RNA 2-1 (vtRNA2-1) is an RNA that has been implicated in some cancers; …
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Elucidating TRPA1 Ion Channel Aberrations in Oesophageal Adenocarcinoma.
… recurrent mutations are observed in only few genes, we have identified TRPA1 (Transient Receptor Potential Ankyrin 1) as a novel driver gene in OAC with recurrent mutations in a sequenced cohort of 551 OAC patients. TRPA1 is a ligand-gated, Calcium (Ca2+) -permeable membrane protein, which has …
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Molecular Pathogenesis of MALT lymphoma
… cell lymphomas were analysed by Affymetrix gene expression microarray platform. Unsupervised clustering showed that cases of MALT lymphoma were clustered as a single branch. However, within the MALT lymphoma group, translocation-positive cases were intermingled with translocation-negative …
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Genome-wide Predictive Simulation on the Effect of Perturbation and the Cause of Phenotypic variations with Network Biology Approach
… technologies such as microarray-based gene expression profiling, a large amount of molecular profile data have been generated in several disease related contexts. Despite the fact that these data likely contain systems-level information about disease regulation, revealing the underlying …
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A multiplexed approach for quantitative profiling of the translatome using bioorthogonal non-canonical amino acids
… adapt it for robust quantitative multiplexing analysis. In the BONCAT method, cells are pulsed with azidohomoalanine (Aha), a methionine analog that contains an azide functional group, such that proteins synthesized for the duration of the pulse incorporate Aha. By coupling pulsed stable …
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The anticipatory unfolded protein response and estrogen receptor mutations in breast cancer
… estrogen-independent and antiestrogen resistant gene expression and cell proliferation. A novel invasion-dissociation-rebinding (IDR) assay demonstrated that the mutant cells have a higher tendency to dissociate from invasion sites and rebind to a second site. Compared to wild type breast tumors, …
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Interpreting transcriptional signatures and their relevance to disease biology, prognosis and treatment resistance in colorectal cancer
… <br/>Colourectal cancer (CRC) is a common heterogeneous malignancy with a number of different disease subtypes influenced by distinct biology. The clinical implications of this disease heterogeneity are likely to influence treatment strategies further in the future. Therefore, patient …
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Bicluster-Based Identification of Gene Sets Through Multivariate Meta-Analysis (MVMA)
… This dissertation is focused on mining of public gene expression data to discover gene sets that may be parts of biological pathways. It tries to answer these two overall questions: (1) what is the data mining method best suited for finding gene sets? (2) how best to utilize multiple datasets in …
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Pax5 Haploinsufficiency Cooperates with BCR-ABL1 to Induce Acute Lymphoblastic Leukemia
… distinct subtypes each with its own unique pathogenesis, clinical behavior, and response to therapy. Chromosomal aberrations are a hallmark of ALL but alone fail to induce leukemia. Pediatric ALLs can be divided into several categories based on the expression of several genetically conserved …
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