GSCA / cGSCA – Gene Set Control Analysis

GSCA / cGSCA

:: DESCRIPTION

GSCA is a new computational framework for linking gene sets with transcriptional control.

C-GSCA tool performs a hierarchical clustering of over-represented samples found by GSCA.

::DEVELOPER

GSCA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Exp Hematol. 2013 Apr;41(4):354-66.e14. doi: 10.1016/j.exphem.2012.11.008. Epub 2012 Dec 4.
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data.
Joshi A1, Hannah R, Diamanti E, Göttgens B.

DBGSA 1.2 – Distance-based Gene Set Functional Enrichment Analysis

DBGSA 1.2

:: DESCRIPTION

DBGSA is a novel distance-based gene set enrichment analysis method.

::DEVELOPER

DBGSA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 DBGSA

:: MORE INFORMATION

Citation

J Hum Genet. 2012 Oct;57(10):642-53. doi: 10.1038/jhg.2012.86. Epub 2012 Jul 12.
DBGSA: a novel method of distance-based gene set analysis.
Li J, Wang L, Xu L, Zhang R, Huang M, Wang K, Xu J, Lv H, Shang Z, Zhang M, Jiang Y, Guo M, Li X.

Confero 0.1 – Integrated Contrast and Gene Set Platform

Confero 0.1

:: DESCRIPTION

Confero is a contrast data and gene set platform for downstream analysis and biological interpretation of omics data.

::DEVELOPER

Confero team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • Perl
  • MySQL Server

:: DOWNLOAD

 Confero

:: MORE INFORMATION

Citaton

BMC Genomics. 2013 Jul 29;14:514. doi: 10.1186/1471-2164-14-514.
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.
Hermida L1, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J.

npGSEA 1.28.0 – Permutation Approximation methods for Gene Set Enrichment Analysis

npGSEA 1.28.0

:: DESCRIPTION

npGSEA  (non-permutation GSEA) calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

::DEVELOPER

Jessica Larson <larson.jess at gmail.com> and Art Owen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 npGSEA

:: MORE INFORMATION

Citation

Moment based gene set tests.
Larson JL, Owen AB.
BMC Bioinformatics. 2015 Apr 28;16(1):132.

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