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.

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

Lee Lab 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.

Moksiskaan 2.04 – Translate Gene Sets to Networks

Moksiskaan 2.04

:: DESCRIPTION

Moksiskaan is a generic database that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. Moksiskaan provides various pathway components for Anduril and may be used to extends its capabilities.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Moksiskaan

:: MORE INFORMATION

Citation

Marko Laakso and Sampsa Hautaniemi
Integrative platform to translate gene sets to networks
Bioinformatics (2010) 26 (14): 1802-1803.

SeqGSEA 1.9.0 – Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

SeqGSEA 1.9.0

:: DESCRIPTION

SeqGSEA generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing.

::DEVELOPER

Xi Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R package
  • BioConductor

:: DOWNLOAD

 SeqGSEA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 6. [Epub ahead of print]
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.
Wang X1, Cairns MJ.

BMC Bioinformatics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2105-14-S5-S16. Epub 2013 Apr 10.
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.
Wang X, Cairns MJ.

StemChecker – Discover and Explore Stemness Signatures in Gene Set

StemChecker

:: 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

  • Web Browser

:: DOWNLOAD

 NO

:: 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

PADOG 1.10.0 – Gene Set Analysis using Gene Expression data

PADOG 1.10.0

:: DESCRIPTION

PADOG (Pathway Analysis with Down-weighting of Overlapping Genes) is a standard Bioconductor style R package that can be used to perform gene set analysis (e.g. pathway analysis) using microarray data.

::DEVELOPER

the Bioinformatics and Computational Biology Unit of the Perinatology Research Branch (NICHD)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package
  • Bioconductor

:: DOWNLOAD

  PADOG

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Jun 19;13:136. doi: 10.1186/1471-2105-13-136.
Down-weighting overlapping genes improves gene set analysis.
Tarca AL, Draghici S, Bhatti G, Romero R.

GSEA 2.2.0 – Gene Set Enrichment Analysis

GSEA 2.2.0

:: DESCRIPTION

GSEA (Gene Set Enrichment Analysis) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

::DEVELOPER

GSEA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GSEA

:: MORE INFORMATION

Citation:

Subramanian, Tamayo, et al. (2005,)
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
PNAS 102, 15545-15550