GeneSetScan 0.021 beta – Scan Genome-wide SNP data for Gene-set Association Analysis

GeneSetScan 0.021 beta

:: DESCRIPTION

GeneSetScan offers a general approach to scan genome-wide SNP data for gene-set association analyses

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneSetScan

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Jan;36(1):3-16. doi: 10.1002/gepi.20632. Epub 2011 Dec 7.
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.
Schaid DJ1, Sinnwell JP, Jenkins GD, McDonnell SK, Ingle JN, Kubo M, Goss PE, Costantino JP, Wickerham DL, Weinshilboum RM.

GSAA 2.0 / GSAA-SNP / GSAA-Seq – Gene Set Association Analysis / Analysis-SNP / for RNA-Seq

GSAA 2.0 / GSAA-SNP / GSAA-Seq

:: DESCRIPTION

GSAA (Gene Set Association Analysis) is a computational method that integrates gene expression analysis with genome wide association studies to determine whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to gene expression profiles and genotypes between two biological states. Gene sets are generally a group of genes that are putatively functionally related, co-regulated, or tightly linked on the same chromosome.

GSAA-SNP (Gene Set Association Analysis-SNP) is a computational method that determines whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to genotypes between two biological states. Gene sets are generally a group of genes that are putatively functionally related, co-regulated, or tightly linked on the same chromosome.

GSAA-Seq (Gene Set Association Analysis for RNA-Seq) is a computational method that evaluates whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to RNA-Seq gene expression profiles between two biological states. Gene sets are generally a group of genes that are putatively functionally related, co-regulated, or tightly linked on the same chromosome.

::DEVELOPER

Furey Lab at The University of North Carolina at Chapel Hill and Mukherjee Lab at Duke University.

:: SCREENSHOTS

GSAA

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  GSAA / GSAA-SNP / GSAA-Seq

:: MORE INFORMATION

Citation

GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.
Xiong Q, Mukherjee S, Furey TS.
Sci Rep. 2014 Sep 12;4:6347. doi: 10.1038/srep06347.

Genome Res. 2012 Feb;22(2):386-97. doi: 10.1101/gr.124370.111. Epub 2011 Sep 22.
Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.
Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS.