Deciphering the scalene association among type‐2 diabetes mellitus, prostate cancer, and chronic myeloid leukemia via enrichment analysis of disease‐gene network
Sign Up to like & getrecommendations! Published in 2019 at "Cancer Medicine"
DOI: 10.1002/cam4.1845
Abstract: The potential biological relationship between type‐2 diabetes mellitus (T2DM) has been focused in numerous studies. To investigate the molecular associations among T2DM, prostate cancer (PCa), and chronic myeloid leukemia (CML), using a biomolecular network enrichment… read more here.
Keywords: enrichment analysis; cml pca; overlapping genes; pca ... See more keywords
Extensive molecular reclassification: new perspectives in small bowel adenocarcinoma?
Sign Up to like & getrecommendations! Published in 2021 at "Medical Oncology"
DOI: 10.1007/s12032-021-01468-z
Abstract: SBA classification is still based on the location of the primary tumor, without genetic information. in the current study, an extensive genetic profile of SBA, was performed in order to identify and quantify targetable alterations… read more here.
Keywords: new perspectives; extensive molecular; enrichment analysis; reclassification new ... See more keywords
RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling
Sign Up to like & getrecommendations! Published in 2022 at "Communications Biology"
DOI: 10.1038/s42003-021-02991-5
Abstract: Changes in a few key transcriptional regulators can lead to different biological states. Extracting the key gene regulators governing a biological state allows us to gain mechanistic insights. Most current tools perform pathway/GO enrichment analysis… read more here.
Keywords: analysis; expression; enrichment analysis; ets transcription ... See more keywords
Pattern enrichment analysis for phage selection of stapled peptide ligands
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DOI: 10.1039/d2sc04058a
Abstract: Phage display is the most widely used technique to discover de novo peptides that bind to target proteins. However, it is associated with some challenges such as compositional bias. In this study, to overcome these… read more here.
Keywords: enrichment analysis; sequence; pattern enrichment; selection ... See more keywords
On the influence of several factors on pathway enrichment analysis
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac143
Abstract: Abstract Pathway enrichment analysis has become a widely used knowledge-based approach for the interpretation of biomedical data. Its popularity has led to an explosion of both enrichment methods and pathway databases. While the elegance of… read more here.
Keywords: enrichment analysis; pathway enrichment; analysis; influence several ... See more keywords
Differential Gene Set Enrichment Analysis: A statistical approach to quantify the relative enrichment of two gene sets.
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa658
Abstract: MOTIVATION Gene Set Enrichment Analysis (GSEA) is an algorithm widely used to identify statistically enriched gene sets in transcriptomic data. However, GSEA cannot examine the enrichment of two gene sets or pathways relative to one… read more here.
Keywords: gene set; enrichment analysis; dgsea; set enrichment ... See more keywords
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac076
Abstract: MOTIVATION The identification of pathways and biological processes from differential gene expression is central for interpretation of data collected by transcriptomics assays. Gene-Set Enrichment Analysis (GSEA) is the most common used algorithm to calculate the… read more here.
Keywords: set enrichment; enrichment analysis; gene set; gene ... See more keywords
CBNplot: Bayesian network plots for enrichment analysis
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac175
Abstract: SUMMARY When investigating gene expression profiles, determining important directed edges between genes can provide valuable insights in addition to identifying differentially expressed genes. In the subsequent functional enrichment analysis (EA), understanding how enriched pathways or… read more here.
Keywords: cbnplot; enrichment analysis; analysis; gene ... See more keywords
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac757
Abstract: Abstract Motivation Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes. However, the currently available tools used to perform GSEA have a limited ability to analyze large datasets, which… read more here.
Keywords: enrichment analysis; gsea; analysis; gseapy ... See more keywords
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways
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DOI: 10.1093/bioinformatics/btac812
Abstract: Noncoding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the existing signaling pathway databases do… read more here.
Keywords: kegg; platform; database; enrichment analysis ... See more keywords
Epigenomic annotation‐based interpretation of genomic data: from enrichment analysis to machine learning
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx414
Abstract: Motivation One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation… read more here.
Keywords: machine learning; interpretation; enrichment analysis; genomic data ... See more keywords