enrichment analysis
An introduction to effective use of enrichment analysis software
... during enrichment analysis and by incorporating a range of annotation types in concert, analysis can be more effective as increased coverage increases analytical power and can provide a more complete ...
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Enrichment analysis applied to disease prognosis
... of enrichment analysis for disease prognosis, as the first component of a prognosis methodology that will assist in the evaluation of patients in respect to the likelihood of suffering a disease-related ...
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Absolute Enrichment: Gene Set Enrichment Analysis for Homeostatic Systems
... The Gene Set Enrichment Analysis (GSEA) identifies sets of genes that are differentially regulated in one direction. Many homeostatic systems will include one limb that is upregulated in response to a ...
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Gene Set Enrichment Analysis using Linear Models and Diagnostics
... careful analysis led us to conclude beyond reasonable doubt, that two females have been misassigned as ...subsequent analysis in this article, we have reassigned two samples to female and one sample to ...
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Gene Set Enrichment Analysis using Linear Models and Diagnostics
... As stated previously, the residuals methods has not been as thoroughly optimized, and offering a competitor to Hertzberg et al. (2007) was not our goal here. However, the similarity in performance is encouraging, given ...
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Abrupt involution induces inflammation, estrogenic signaling, and hyperplasia linking lack of breastfeeding with increased risk of breast cancer
... gene enrichment in parous women who breastfed < 6 months ...expression analysis using Human Transcriptome Array ...set enrichment analysis (GSEA; ...
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RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans
... The enrichment of such processes in this category of regulated genes reflects the fact that metabolic functions (glycolysis and respiration), biosynthesis of cellular FIG 4 Identification of ...
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Original Article Exploring the multiple miliary osteoma cutis-related genes by gene expression analysis
... To explore the key genes in the pathogenesis of MMOC, skin biopsies from three patients and two controls were used to analyze the expression profile. In this study, microarray data had been selected for differential ...
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Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma
... pathway enrichment analysis GO and KEGG functional enrichment analyses of the genes in the lightyellow and pink modules were performed using the “ClusterProfiler” package in R (Additional file 3: ...
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The Relationship Between Long-Range Chromatin Occupancy and Polymerization of the Drosophila ETS Family Transcriptional Repressor Yan
... motif enrichment analysis using CentriMo, a visualization and statistical analysis tool that identifies the region of maximum central enrichment in a set of ChIP-seq peak regions and displays ...
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Identification of ageing-associated naturally occurring peptides in human urine
... pathway enrichment analysis incorporating the 112 identified peptides and 32 predicted proteases suggested molecular pathways that are affected in normal and pathological ...The enrichment ...
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Pathway analysis reveals functional convergence of gene expression profiles in breast cancer
... same analysis in a single data set and identified many lists of genes equally predictive of the ...gene-set analysis include the Gene Set Enrichment Analysis (GSEA) [8], Significance ...
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<p>Gene expression profiling reveals candidate biomarkers and probable molecular mechanism in diabetic peripheral neuropathy</p>
... associated with demyelination may conduce to a better understanding of DPN and fi nding the predictive biomar- kers of this disease. In 2010, Hur et al, analyzed genes that differed between DPN progressors and ...
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Anti-tumor effects and potential therapeutic response biomarkers in α-emitting meta-211At-astato-benzylguanidine therapy for malignant pheochromocytoma explored by RNA-sequencing
... pathway enrichment analysis, reference genes were first matched to KEGG (Kyoto Encyclop- edia of Genes and Genomes) orthology using the KEGG KAAS web service [23], and enrichment of pathways for each ...
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CSgator: an integrated web platform for compound set analysis
... Set Enrichment Analysis; CC: Compound Cluster; CCA : Compound Cluster Analysis; HEA: Hit Enriched Assay; ES: enrichment score; LLR: log likelihood ratio; OR: odds ratio; MDS: multidimensional ...
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Differentially expressed genes between systemic sclerosis and rheumatoid arthritis
... (GO) enrichment analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to perform func- tional enrichment analysis and identify important bio- logical pathways related ...
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Original Article Identification of key genes associated with idiopathic pulmonary fibrosis using bioinformatics analysis
... thway enrichment analysis, genes in this module were mainly involved in ECM-rece- ptor interaction (P = ...nal enrichment analysis, the D1, CCND1) were TAGs (including 2 oncogenes, ...
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Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
... Methods: RNA sequencing was performed using the lung adenocarcinoma cell line A549 after no treatment or treatment with X-ray or X-ray + HPD. The differentially expressed genes (DEGs) were screened using Mfuzz package by ...
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A Theory of Genetic Analysis Using Transcriptomic Phenotypes
... GO enrichment analysis is that it is often difficult to interpret due to the large number of terms associated with a given gene (which we refer to as ‘result ...GO enrichment analysis, ...
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Original Article Identifying key genes in rheumatoid arthritis using bioinformatics analysis
... functional enrichment analysis of the DEGs was performed using ...GO analysis showed that the upregulated genes were mainly enriched in the inflammatory response, but the downregulated genes were ...
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