TopoGSA – Network Topological Gene Set Analysis

TopoGSA

:: 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

TopoGSA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: 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.

WebGestalt 2019 – WEB-based GEne SeT AnaLysis Toolkit

WebGestalt 2019

:: 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

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: 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.

GSDCA – Gene Set Differential Coordination Analysis

GSDCA

:: 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

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

GSDCA

:: 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.

NGSEA – Network-augmented Gene Set Enrichment analysis tool

NGSEA

:: 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

  • Web browser

:: DOWNLOAD

 NO

:: 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

RIDDLE – Network-assisted Gene Set Analysis

RIDDLE

:: DESCRIPTION

RIDDLE (Reflective diffusion and local extension)is a network-based method for characterizing gene sets. It asks if an input query set is significantly “close” to a known pathway or disease set in the human functional network.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 26;13(12):R125. doi: 10.1186/gb-2012-13-12-r125.
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network.
Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM.

PAEA – Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool

PAEA

:: 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

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: 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.

GSCA 2.0 – Gene Set Context Analysis

GSCA 2.0

:: DESCRIPTION

GSCA is an open source software package to transform massive amounts of Publicly available gene Expression Data (PED) into a tool for making new discoveries.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 GSCA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 Jan 8;44(1):e8. doi: 10.1093/nar/gkv873. Epub 2015 Sep 8.
Turning publicly available gene expression data into discoveries using gene set context analysis.
Ji Z, Vokes SA, Dang CV, Ji H

WhichGenes 1.5 – Gene Set building tool

WhichGenes 1.5

:: DESCRIPTION

WhichGenes is a powerful gene set building tool. It allows the user to extract lists of genes from multiple sources in order to use them for further experiments.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

 WhichGenes

:: MORE INFORMATION

Citation

Glez-Peña,D., Gómez-López,G., Pisano,D.G., Fdez-Riverola,F. (2009).
WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis.
Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp263

GeneTrail / GeneTrailExpress – Gene Set Analysis tool / for pre-processing Microarray data

GeneTrail / GeneTrailExpress

:: DESCRIPTION

GeneTrail is a comprehensive and efficient gene set analysis tool that offers a rich functionality and is easy to use.

GeneTrailExpress provides comprehensive normalization and scoring functions for pre-processing microarray data. The processed data is directly passed to GeneTrail for statistical evaluation in an extensive gene set analysis.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Dec 22;9:552. doi: 10.1186/1471-2105-9-552.
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
Keller A1, Backes C, Al-Awadhi M, Gerasch A, Küntzer J, Kohlbacher O, Kaufmann M, Lenhof HP.

Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP.
GeneTrail–advanced gene set enrichment analysis.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92.

rcNet – Web Tool for Inferring Disease and Gene Set Association

rcNet

:: DESCRIPTION

rcNet (Rank Coherence in Networks) web tool provides an online resource to predict associations between disease phenotypes and gene sets. rcNet algorithms combine known disease-gene associations in OMIM with the topological information in the disease phenotype similarity network and the gene-gene interaction network to analyze the association between a gene set and disease phenotypes. The networks provide richer and more reliable information for computing the association scores used to rank the phenotypes. reNet algorithms could be applied to validate and analyze the candidate disease gene identified in GWAS, DNA copy number analysis, and Microarray gene expression profiling.

::DEVELOPER

Kuang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Matlab

:: DOWNLOAD

 rcNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.
Inferring disease and gene set associations with rank coherence in networks.
Hwang T, Zhang W, Xie M, Liu J, Kuang R.