Tag: Gene-set

GSEA 4.1.0 – Gene Set Enrichment Analysis

GSEA 4.1.0

:: 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

PADOG 1.34.0 – Gene Set Analysis using Gene Expression data

PADOG 1.34.0

:: 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.

SeqGSEA 1.33.0 – Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

SeqGSEA 1.33.0

:: 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.

GeneTrail 3.0 – Gene Set Analysis tool / for pre-processing Microarray data

GeneTrail 3.0

:: DESCRIPTION

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

::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.

mGSZ 1.0 / GSZ – Gene Set Analysis methods based on GSZ Statistics

mGSZ 1.0 / GSZ

:: DESCRIPTION

mGSZ is a gene set analysis method based on GSZ (Gene Set Z-score) statistics and asymptotic p-value. mGSZ is different from the standard GSZ method in that it assigns asymptotic p-values to the gene set scores instead of empirical p-values.

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R / MatLab

:: DOWNLOAD

 mGSZ

:: MORE INFORMATION

Citation:

Gene Set Analysis: Limitations in popular existing methods and proposed improvements.
Mishra P, Törönen P, Leino Y, Holm L.
Bioinformatics. 2014 Jun 5. pii: btu374.

BMC Bioinformatics. 2009 Sep 23;10:307. doi: 10.1186/1471-2105-10-307.
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.
Törönen P1, Ojala PJ, Marttinen P, Holm L.

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

GeneCommittee – Testing the Discriminatory Power of Gene Sets in Microarray data Classification

GeneCommittee

:: DESCRIPTION

GeneCommittee is a web-based interactive tool for giving specific support to the study of the discriminative classification power of custom hypothesis in the form of biological relevant gene sets.

::DEVELOPER

Sistemas Informáticos de Nueva Generación, UA.PT Bioinformatics

:: SCREENSHOTS

 N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jan 30;15:31. doi: 10.1186/1471-2105-15-31.
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.
Reboiro-Jato M, Arrais JP, Oliveira JL, Fdez-Riverola F1

SiGPAT 0.1 – Finding significant Expression Patterns of Gene Set

SiGPAT 0.1

:: DESCRIPTION

SiGPAT is a useful tool based on gene set analysis for microarray data. It can find significant expression patterns of gene sets by pri-defined biological knowledge. To be unique to other tools, SiGPAT assignes two statistics for each gene sets and classifies expression patterns of gene sets form two dimension distribution of set-level statistics. The tool was evaluated with better performance than current tools such as GSEA and SAM-GS

::DEVELOPER

Zuguang Gu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

  SiGPAT

:: MORE INFORMATION

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

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.

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