:: DESCRIPTION
MGSA (model-based gene set analysis) is an effective alternative to classical gene set enrichment analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Model-based gene set analysis for Bioconductor.
Bauer S, Robinson PN, Gagneur J.
Bioinformatics. 2011 Jul 1;27(13):1882-3. doi: 10.1093/bioinformatics/btr296
:: DESCRIPTION
MEGA-V is an open-source R application with a Shiny web interface. It identifies gene sets with a significantly higher number of variants in a cohort of interest (cohort A) as compared to (1) a control cohort (cohort B) or (2) a random distribution generated using Monte Carlo.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gambardella G, Cereda M, Benedetti L, Ciccarelli FD.
MEGA-V: detection of variant gene sets in patient cohorts.
Bioinformatics. 2017 Apr 15;33(8):1248-1249. doi: 10.1093/bioinformatics/btw809. PMID: 28003259; PMCID: PMC5408849.
:: DESCRIPTION
StemChecker is a web-server that enables researchers to rapidly check whether a given list of genes can be associated with stemness.
::DEVELOPER
Systems Biology and Bioinformatics Laboratory @ University of Algarve
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RS, Machado S, Pacheco-Leyva I, Duarte I, Futschik ME.
Nucleic Acids Res. 2015 May 24. pii: gkv529
:: DESCRIPTION
Broad-Enrich tests sets of broad genomic regions (e.g., from ChIP-seq data for histone modifications or copy number variations) for enriched biological pathways, Gene Ontology terms, or other gene sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Broad-Enrich: functional interpretation of large sets of broad genomic regions.
Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ, Sartor MA.
Bioinformatics. 2014 Sep 1;30(17):i393-i400. doi: 10.1093/bioinformatics/btu444.
:: DESCRIPTION
ChIP-Enrich tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology terms, and other types of gene sets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ChIP-Enrich: gene set enrichment testing for ChIP-seq data.
Welch RP, Lee C, Imbriano PM, Patil S, Weymouth TE, Smith RA, Scott LJ, Sartor MA.
Nucleic Acids Res. 2014 May 30. pii: gku463.
:: DESCRIPTION
PAEA (Principal Angle Enrichment Analysis) is a new multivariate approach to gene-set enrichment which uses the geometrical concept of the principal angle to quantify gene-set enrichment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proceedings (IEEE Int Conf Bioinformatics Biomed). 2015 Nov;2015:256-262.
Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.
Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR1, Ma’ayan A.
:: DESCRIPTION
TopoGSA (Topology-based Gene Set Analysis) computes and visualise the topological properties of a set of genes/proteins mapped onto a molecular interaction network. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, are computed and compared against those of known cellular pathways and processes (KEGG, BioCarta, GO, etc.).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2010 May 1;26(9):1271-2. doi: 10.1093/bioinformatics/btq131. Epub 2010 Mar 24.
TopoGSA: network topological gene set analysis.
Glaab E, Baudot A, Krasnogor N, Valencia A.
:: DESCRIPTION
WebGestalt is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W77-83. doi: 10.1093/nar/gkt439. Epub 2013 May 23.
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013.
Wang J1, Duncan D, Shi Z, Zhang B.
:: DESCRIPTION
GSDCA finds gene sets that are differentially coordinated with the rest of the genome between treatment conditions. It also finds differentially coordinated gene set pairs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genomics. 2011 Dec;98(6):469-77. doi: 10.1016/j.ygeno.2011.09.001.
Capturing changes in gene expression dynamics by gene set differential coordination analysis.
Yu T, Bai Y.
:: DESCRIPTION
NGSEA (network-based GSEA) measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network.
::DEVELOPER
Network Biomedicine Laboratory at Yonsei University, Korea
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cells. 2019 Aug 31;42(8):579-588. doi: 10.14348/molcells.2019.0065.
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets.
Han H, Lee S, Lee I
