De Novo Pathway Enrichment with KeyPathwayMiner
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9873-9_14
Abstract: Biomolecular networks such as protein-protein interaction networks provide a static picture of the interplay of genes and their products, and, consequently, they fail to capture dynamic changes taking place during the development of complex diseases.… read more here.
Keywords: keypathwayminer; biology; pathway enrichment; enrichment keypathwayminer ... See more keywords
SomaModules: A Pathway Enrichment Approach Tailored to SomaScan Data
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Proteome Research"
DOI: 10.1021/acs.jproteome.4c01114
Abstract: Motivated by the lack of adequate tools to perform pathway enrichment analysis, this work presents an approach specifically tailored to SomaScan data. Starting from annotated gene sets, we developed a greedy, top-down procedure to iteratively… read more here.
Keywords: tailored somascan; somascan data; gene sets; enrichment analysis ... 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
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac553
Abstract: BACKGROUND Global or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses to exposures or interactions with microbial communities. However, biological interpretation of global metabolomics… read more here.
Keywords: enrichment methods; metabolomics data; pathway enrichment; functional interpretation ... See more keywords
PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework
Sign Up to like & getrecommendations! Published in 2025 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaf590
Abstract: Abstract Motivation Pathway enrichment analysis is commonly used to interpret epigenomewide association studies, yet conventional methods often rely on arbitrary thresholds and simplified CpG–gene mappings, making them sensitive to analytical choices and unable to fully… read more here.
Keywords: methylation; dna methylation; pathwayvote package; package ... See more keywords
Abstract 6313: Context-aware pathway enrichment clustering and interpretation using large language models
Sign Up to like & getrecommendations! Published in 2025 at "Cancer Research"
DOI: 10.1158/1538-7445.am2025-6313
Abstract: Pathway enrichment analysis is pivotal for elucidating key oncogenic processes from high-throughput cancer profiling. However, the inherent redundancy and interdependence in biological pathway annotations complicate the meaningful interpretation of enrichment results. This challenge necessitates the… read more here.
Keywords: context aware; language; cancer; pathway enrichment ... See more keywords
Nine quick tips for pathway enrichment analysis
Sign Up to like & getrecommendations! Published in 2022 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1010348
Abstract: Pathway enrichment analysis (PEA) is a computational biology method that identifies biological functions that are overrepresented in a group of genes more than would be expected by chance and ranks these functions by relevance. The… read more here.
Keywords: quick tips; enrichment analysis; nine quick; pathway enrichment ... See more keywords
An integrative analysis of an lncRNA–mRNA competing endogenous RNA network to identify functional lncRNAs in uterine leiomyomas with RNA sequencing
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2022.1053845
Abstract: Objective: To explore the functions of mRNAs and lncRNAs in the occurrence of uterine leiomyomas (ULs) and further clarify the pathogenesis of UL by detecting the differential expression of mRNAs and lncRNAs in 10 cases… read more here.
Keywords: network; rna sequencing; rna; pathway enrichment ... See more keywords
Metabolomic Profiling Reveals Distinct Signatures in Primary and Secondary Polycythemia
Sign Up to like & getrecommendations! Published in 2025 at "Metabolites"
DOI: 10.3390/metabo15090630
Abstract: Background/Objectives: The differential diagnosis between primary polycythemia vera (PV) and secondary polycythemia (SP) presents significant clinical challenges owing to substantial phenotypic overlap. This investigation utilized untargeted metabolomic approaches to elucidate disease-specific metabolic perturbations and evaluate… read more here.
Keywords: secondary polycythemia; polycythemia; analysis; metabolomic profiling ... See more keywords