Tag: Gene-set

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.

PhenoFam – Gene Set Enrichment Analysis in the Protein Domain Context

PhenoFam

:: DESCRIPTION

PhenoFam performs gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. The tool is designed to analyse complete sets of results from quantitative high-throughput studies (gene expression microarrays, functional RNAi screens, etc.) without prior pre-filtering or hits-selection steps.

::DEVELOPER

Frank Buchholz , Max Planck Institute of Molecular Cell Biology and Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 PhenoFam

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 17;11:254. doi: 10.1186/1471-2105-11-254.
PhenoFam – gene set enrichment analysis through protein structural information.
Paszkowski-Rogacz M, Slabicki M, Pisabarro MT, Buchholz F.

i-GSEA4GWAS 1.1 – Improved-Gene Set Enrichment Analysis for Genome-Wide Association Study

i-GSEA4GWAS 1.1

:: DESCRIPTION

The i-GSEA4GWAS (improved GSEA for GWAS) web server is a web-based resource for analysis of GWAS data (typically each SNP’s -log(P-value)) to identify pathways/gene sets correlated to certain traits by implementing an improved Gene Set Enrichment Analysis (i-GSEA) approach. i-GSEA4GWAS aims to establish an open platform to help further interpret the GWAS data to provide new insights in complex disease study, especially in complementation to the standard single variant/gene based analysis.

::DEVELOPER

Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

   i-GSEA4GWAS

:: MORE INFORMATION

Citation

i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study.
Kunlin Zhang; Sijia Cui; Suhua Chang; Liuyan Zhang; Jing Wang
Nucleic Acids Research 2010; doi: 10.1093/nar/gkq324

dCoxS – Biological Interpretation of Paired Gene Sets

dCoxS

:: DESCRIPTION

dCoxS (differentially coexpressed gene sets) is a software that identifies the differentially coexpressed gene set pairs between conditions.

::DEVELOPER

SNUBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  dCoxS

:: MORE INFORMATION

Citation

Sung Bum Cho, Jihun Kim and Ju Han Kim
Identifying Set-wise Differential Co-expression in Gene Expression Microarray Data
BMC Bioinformatics 2009, 10:109 doi:10.1186/1471-2105-10-109

 

RssGsc 1.1 – Selecting Interesting Gene Sets

RssGsc 1.1

:: DESCRIPTION

RssGsc (Rank Sum Statistics for Gene Set Collections  ) is a bio-informatics tool. This tool allows to perform enrichment analysis of gene sets, that is, to identify biologically meaningful gene sets from a ranked list of genes (experimental data).

::DEVELOPER

Pablo Cingolani

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 RssGsc

:: MORE INFORMATION

Sub-GSE – Testing Gene Set Enrichment for Subset of Genes

Sub-GSE

:: DESCRIPTION

SubGSE is developed for gene set enrichment analysis.The primary objective of this program is to measure the enrichment of differentially expressed or phenotype associated genes in given gene sets. The input for the program includes the gene expression data of several samples with corresponding phenotypic data (categorical or continuous), and several given gene sets. The program will assess the significance of the enrichment of genes, whose gene expression profiles are associated with the phenotypic data, in each given gene set.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  SubGSE

:: MORE INFORMATION

Citation

Xiting Yan and Fengzhu Sun
Testing gene set enrichment for subset of genes: Sub-GSE
BMC Bioinformatics 2008, 9:362