Tag: Gene Module

OncodriveFM 1.0 – Uncover Driver Genes or Gene Modules

OncodriveFM 1.0

:: DESCRIPTION

Oncodrive-FM detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl
  • R package

:: DOWNLOAD

 OncodriveFM

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Nov;40(21):e169. doi: 10.1093/nar/gks743. Epub 2012 Aug 16.
Functional impact bias reveals cancer drivers.
Gonzalez-Perez A, Lopez-Bigas N.

GRAM 0.6 – Discovery of Gene Modules and Regulatory Networks

GRAM 0.6

:: DESCRIPTION

GRAM (Genetic RegulAtory Modules) identifies modules, collections of genes that share common regulators as well as expression profiles.

::DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

GRAM

:: MORE INFORMATION

Citation

Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.
Computational discovery of gene modules and regulatory networks.
Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

ClustEx 2.0 – Responsive Gene Module Identification package

ClustEx 2.0

:: DESCRIPTION

ClustEx, a two-step method based on the new formulation, was developed and applied to identify the responsive gene modules of human umbilical vein endothelial cells (HUVECs) in inflammation and angiogenesis models by integrating the time-course microarray data and genome-wide PPI data. It shows better performance than several available module identification tools by testing on the reference responsive gene sets. Gene set analysis of KEGG pathways, GO terms and microRNAs (miRNAs) target gene sets further supports the ClustEx predictions.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  ClustEx

:: MORE INFORMATION

Citation

Jin Gu, Yang Chen, Shao Li, Yanda Li.
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis.
BMC Systems Biology 2010, 4:47.