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Gene set enrichment analysis

Gene-set enrichment analysis of differentially expressed genes in the transcriptome of the human corneal endothelium in association with age effect

Gene-set enrichment analysis of differentially expressed genes in the transcriptome of the human corneal endothelium in association with age effect

... pathways. Gene set enrichment analysis using available software like Enrichr Mayaan Laboratory enables us to understand the transcription factors, pathways, ontologies, proteins, diseases and ...

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FDR-FET: an optimizing gene set enrichment analysis method

FDR-FET: an optimizing gene set enrichment analysis method

... gene set enrichment analysis, we analyzed the regulated gene list generated with an arbitrary FDR cutoff ...significant gene set hits calculated by FDR-FET using reference ...

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Absolute Enrichment: Gene Set Enrichment Analysis for Homeostatic Systems

Absolute Enrichment: Gene Set Enrichment Analysis for Homeostatic Systems

... The Gene Set Enrichment Analysis (GSEA) (1) is a powerful technique for elucidating various groups of genes that may be important from gene expression data ...identifies gene ...

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A cross-study gene set enrichment analysis identifies critical pathways in endometriosis

A cross-study gene set enrichment analysis identifies critical pathways in endometriosis

... performed gene set enrichment analysis of six independent publicly available gene expression data sets to understand in depth the common biological mecha- nisms involved in ...the ...

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Gene Set Enrichment Analysis using Linear Models and Diagnostics

Gene Set Enrichment Analysis using Linear Models and Diagnostics

... There exist more aggressive weighting schemes and sophisticated algorithms, such as Yohai (1987)’s MM-estimator which identifies outliers more aggressively – with the almost inevitable side- effect of more false ...

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Gene Set Enrichment Analysis using Linear Models and Diagnostics

Gene Set Enrichment Analysis using Linear Models and Diagnostics

... the gene-expression case, where we run a large number of identical models in parallel, we will show that residuals can also be used to identify genes or samples with discrepant or unusual residual patterns across ...

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Molecular spectrum of BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias: implication for MEK-ERK pathway activation

Molecular spectrum of BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias: implication for MEK-ERK pathway activation

... the gene expression profiles of U266 cells treated with vemurafenib (30 μM) or DMSO for 12 ...hours. Gene set enrichment analysis (GSEA) was used to identify a priori defined sets of ...

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Abrupt involution induces inflammation, estrogenic signaling, and hyperplasia linking lack of breastfeeding with increased risk of breast cancer

Abrupt involution induces inflammation, estrogenic signaling, and hyperplasia linking lack of breastfeeding with increased risk of breast cancer

... analyze gene enrichment in parous women who breastfed < 6 months ...utilized gene ex- pression data obtained from women who were undergo- ing reduction mammoplasty and were enrolled in the tissue ...

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Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology

Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology

... the gene expression omnibus dataset uploaded to the NCBI from a whole-genome gene expression analysis carried out at Mayo Clinic in Rochester, ...ones. Gene Set Enrichment ...

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Dynamic Interactions between Bombyx mori Nucleopolyhedrovirus and Its Host Cells Revealed by Transcriptome Analysis

Dynamic Interactions between Bombyx mori Nucleopolyhedrovirus and Its Host Cells Revealed by Transcriptome Analysis

... profile gene expression during baculovirus infection, the response of host genes to baculovirus infection and the interaction between baculovirus and its host remain largely ...digital gene expression ...

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ADH genes were examined. ADH mRNA expression level was markedly reduced in HBV-related HCC tumor tissue. ADH1C and ADH5 overexpres-

ADH genes were examined. ADH mRNA expression level was markedly reduced in HBV-related HCC tumor tissue. ADH1C and ADH5 overexpres-

... ADH gene expression in hepatitis B virus (HBV)-related hepato- cellular carcinoma ...Microarray analysis and survival profiles of HBV-related HCC from GSE14520 were used to assess the association between ...

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PubMedCentral-PMC5037457.pdf

PubMedCentral-PMC5037457.pdf

... ANOVA analysis with a p-value cut-off ≤ ...functional enrichment analysis was performed with the aim of identifying biological processes, cellular components, or molecular functions that are ...

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TRIM66 overexpresssion contributes to osteosarcoma carcin­ ogenesis and indicates poor survival outcome

TRIM66 overexpresssion contributes to osteosarcoma carcin­ ogenesis and indicates poor survival outcome

... characteristics analysis showed that high expression level of TRIM66 was associated with local recurrence, lung metastasis and poor survival rate in patients with ...Furthermore, gene set ...

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A centrosome clustering protein, KIFC1, predicts aggressive disease course in serous ovarian adenocarcinomas

A centrosome clustering protein, KIFC1, predicts aggressive disease course in serous ovarian adenocarcinomas

... Also, gene expression levels of KIFC1 in high-grade serous ovarian carcinoma (HGSOC) highly correlated with expression of genes driving centrosome amplification (CA), as examined in publically-available ...pathway ...

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Integrated whole genome microarray analysis and immunohistochemical assay identifies COL11A1, GJB2 and CTRL as predictive biomarkers for pancreatic cancer

Integrated whole genome microarray analysis and immunohistochemical assay identifies COL11A1, GJB2 and CTRL as predictive biomarkers for pancreatic cancer

... GEO: Gene Expression Omnibus; GSEA: Gene Set Enrichment Analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; PPI: protein– protein interaction; ROC: ...

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Original Article Integrated regulatory mechanisms of miRNAs and targeted genes involved in colorectal cancer

Original Article Integrated regulatory mechanisms of miRNAs and targeted genes involved in colorectal cancer

... Abstract: Purpose: CRC (Colorectal cancer) is a lethal cancer for death worldwide and the underlying pathological mechanisms for CRC progression remain unclear. We aimed to explore the regulatory mechanism of CRC and ...

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A subset of CD163+ macrophages displays mixed polarizations in discoid lupus skin

A subset of CD163+ macrophages displays mixed polarizations in discoid lupus skin

... skin. Gene set enrichment analysis comparing differentially expressed genes in DLE and normal skin with previously published gene sets associated with M1 and M2 macrophages showed ...

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Hypermethylated KLF9 Is An Independent Prognostic Factor For Favorable Outcome In Breast Cancer

<p>Hypermethylated <em>KLF9</em> Is An Independent Prognostic Factor For Favorable Outcome In Breast Cancer</p>

... Background and objective: Breast cancer (BC) is the most lethal human malignancy and is the leading cause of cancer-associated death in women worldwide. Krüppel-like factor 9 (KLF9) belongs to a family of transcriptional ...

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Ten hub genes associated with progression and prognosis of pancreatic carcinoma identified by co-expression analysis

Ten hub genes associated with progression and prognosis of pancreatic carcinoma identified by co-expression analysis

... from Gene Expression Omnibus (GEO) database ...training set to construct co-expression networks and identify hub genes in our study ...validation set to perform gene set ...

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Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

... Upregulated gene expression during trophoblast differentiation reflects selective expansion of accessible chromatin ...in gene expression profiles were detectable during TSC differentiation ...S5). ...

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