Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data
Background: Global or untargeted metabolomics is widely used to comprehensively
investigate metabolic profiles under various pathophysiological conditions such as …
investigate metabolic profiles under various pathophysiological conditions such as …
Gene set analysis: challenges, opportunities, and future research
Gene set analysis methods are widely used to provide insight into high-throughput gene
expression data. There are many gene set analysis methods available. These methods rely …
expression data. There are many gene set analysis methods available. These methods rely …
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis
Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight
from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class …
from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class …
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs
WebGestalt is a popular tool for the interpretation of gene lists derived from large scale-
omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers …
omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers …
g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)
U Raudvere, L Kolberg, I Kuzmin, T Arak… - Nucleic acids …, 2019 - academic.oup.com
Biological data analysis often deals with lists of genes arising from various studies. The g:
Profiler toolset is widely used for finding biological categories enriched in gene lists …
Profiler toolset is widely used for finding biological categories enriched in gene lists …
Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …
generated from genome-scale (omics) experiments. This method identifies biological …
The gene ontology resource: 20 years and still GOing strong
Gene Ontology Consortium - Nucleic acids research, 2019 - academic.oup.com
Abstract The Gene Ontology resource (GO; http://geneontology. org) provides structured,
computable knowledge regarding the functions of genes and gene products. Founded in …
computable knowledge regarding the functions of genes and gene products. Founded in …
ShinyGO: a graphical gene-set enrichment tool for animals and plants
Motivation Gene lists are routinely produced from various omic studies. Enrichment analysis
can link these gene lists with underlying molecular pathways and functional categories such …
can link these gene lists with underlying molecular pathways and functional categories such …
Integrated omics: tools, advances and future approaches
With the rapid adoption of high-throughput omic approaches to analyze biological samples
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …
such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can …
WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit
Functional enrichment analysis has played a key role in the biological interpretation of high-
throughput omics data. As a long-standing and widely used web application for functional …
throughput omics data. As a long-standing and widely used web application for functional …