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 130 for “"Enrichment analysis"”.
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Integration of Functional Enrichment Analysis Techniques
Η λειτουργική ανάλυση εμπλουτισμού αποτελεί βασικό εργαλείο ερμηνείας ομικών πειραμάτων. Ωστόσο, τα αποτελέσματα της επηρεάζονται σημαντικά από μια σειρά αναλυτικών επιλογών που σπάνια τεκμηριώνονται: ποιο εργαλείο χρησιμοποιείται, πώς ορίζεται το σύνολο αναφοράς, ποιες βάσεις γνώσης ερωτώνται, …
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Using co-expression to redefine functional gene sets for gene set enrichment analysis
… Database (MSigDB) for use with Gene Set Enrichment Analysis (GSEA). We examined the manually curated gene sets in context of an atlas of gene expression of many normal human tissues. To refine gene sets, we clustered the genes in each set based on co-expression across the tissues 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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Teak: A Novel Computational And Gui Software Pipeline For Reconstructing Biological Networks, Detecting Activated Biological Subnetworks, And Querying Biological Networks.
… data accumulation far exceeds the rate of data analysis. There is a need for computational frameworks to bridge the gap and assist researchers in their tasks. The Topology Enrichment Analysis frameworK (TEAK) is an open source GUI and software pipeline that seeks to be one of many tools that …
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Study of proteins after recovery from bacterial infection
… gain insights through differential detection and enrichment analysis. Detection relied on tandem mass spectrometry proteomics. The database search software PEAKS was used to detect peptides and proteins in the treated and control samples. Differential detection was performed using SAS procedures …
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A histopathological and genomics study of the mutated human FAM111B gene related POIKTMP disease
… lung and skin POIKTMP patient tissues. Gene-set enrichment analysis (GSEA) using Enrichr, a computational GSEA tool, was used to predict enrichment analysis between the identified upregulated fibrosis markers and the FAM111B gene. Finally, Immunohistochemistry was used to identify cellular and …
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A histopathological and genomics study of the mutated human FAM111B gene related POIKTMP disease
… lung and skin POIKTMP patient tissues. Gene-set enrichment analysis (GSEA) using Enrichr, a computational GSEA tool, was used to predict enrichment analysis between the identified upregulated fibrosis markers and the FAM111B gene. Finally, Immunohistochemistry was used to identify cellular and …
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Bioinformatics characterization of the molecular pathways impacted by immune challenges in the amygdala
… MIA and control pigs within sex. Functional enrichment analysis provided insight into affected pathways, while protein-protein interaction networks identified non-canonical relationships impacted by MIA. Additionally, complementary analyses, such as transcription factor enrichment analysis, …
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PharMeBINet: a general-Purpose approach for the integration of heterogeneous biomedical data Sources and its application to drug-drug interaction prediction
… increase in data causes problems for storage and analysis. As a solution, data is combined into databases, resulting in an increase in the number of biomedical databases in the last years. For some analyses, a combination of multiple databases is needed to gather all information relevant to …
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Pareto Task Inference Analysis of Single-Cell RNASequencing of Human Placenta Reveals Biological Insightsinto Adverse Pregnancy Outcomes
… of trophoblasts. Marker genes and gene set enrichment analysis for the ParTI polytope vertices, called archetypes, were performed to assess the biological states associated with the archetypes. We demonstrated that the ParTI polytope can separate both broad cell lineages and sublineages, …
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Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing
… (e.g. alternative splicing). Gene Ontology (GO) enrichment analysis revealed massive down-regulation of cell division and cell cycle genes in the drought stressed ovary only. Among GO categories related to carbohydrate metabolism, changes in starch and sucrose metabolism-related genes occurred in …
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Bridging the gap between protein-tyrosine phosphorylation networks, metabolism and physiology in liver-specific PTP1b deletion mice
… and high-fat diet conditions. A phosphosite set enrichment analysis was developed to identify numerous pathways exhibiting PTPlb- and diet-dependent phosphotyrosine regulation. Detection of PTP lb-dependent phosphotyrosine sites on lipid metabolic proteins initiated global lipidomics …
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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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Modeling colorectal cancer initiation using human iPSC-derived intestinal organoids
… and bulk-RNA sequencing. Principle component analysis and Heatmaps were generated from bulk-RNA sequencing for enrichment analysis. RESULTS: Gel electrophoresis revealed biallelic integration of mutant EGFR and KRAS whereas CTNNB1 exhibited monoallelic integration, potentially impacting the …
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Bioinformatics analysis of liver and adipose tissue microarray data from periparturient dairy cattle and development of a web-based ruminant specific microarray database
… several bioinformatics techniques such as gene enrichment analysis or over-represented approach (ORA).The ORA analysis is widely-used in scientific community for functional analysis of high-throughput data such as microarray or RNA-sequencing. It is performed to associate gene sets with their …
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Predicting drug - target interaction network using deep learning models for drug repurposing through genetic information
… learning approaches, such as logistic regression analysis, cannot analyze these data efficiently. To overcome this issue, we proposed a deep neural network model compared with logistic regression and LASSO-based regularized linear classification models to predict drug-target interactions, which …
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Identifying the Role of Transcription Factor RFX3 in 9PDeletion Syndrome
… lines was analyzed using Principal Component Analysis, Differential Gene Expression analysis, and Functional Enrichment analysis. The findings indicate that RFX3 plays a significant role but is not the sole driver of the neuronal phenotypes. SMARCA2, a gene linked to intellectual disability …
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SEA: a novel computational and GUI software pipeline for detecting activated biological sub-pathways
… different pathways using differential expression analysis. Unfortunately, they do not adequately capture the relationships of the genes amongst one another. Structure Enrichment Analysis (SEA) thus seeks to take biological analysis to the next level. SEA accomplishes this goal by highlighting for …
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Feasibility study of compact Neutron Resonance Transmission Analysis using a linac, a fusion-based neutron generator, and an isotopic source
… nuclear security applications such as fuel enrichment analysis and warhead verification seek to identify nuclear materials in a black box target. Neutron Resonance Transmission Analysis (NRTA) is a spectroscopic technique which uses resonant neutron absorption to identify isotopic …
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