Tag: Expression Data

Rankgene 1.1 – Rank Genes from Expression data

Rankgene 1.1

:: DESCRIPTION

 Rankgene is a program for analyzing gene expression data, feature selection and ranking genes based on the predictive power of each gene to classify samples into functional or disease categories.

::DEVELOPER

Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Rankgene

:: MORE INFORMATION

Citation:

RankGene: identification of diagnostic genes based on expression data.
Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S.
Bioinformatics. 2003 Aug 12;19(12):1578-9.

GEMS 1.5 – Biclustering Analysis of Expression data

GEMS 1.5

:: DESCRIPTION

GEMS (Gene Expression Mining Server) is a software for biclustering microarray data. Users may upload expression data and specify a set of criteria. GEMS then performs bicluster mining based on a Gibbs sampling paradigm. The web server provides a flexible and an useful platform for the discovery of co-expressed and potentially co-regulated gene modules

::DEVELOPER

Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 GEMS

:: MORE INFORMATION

Citation:

GEMS: a web server for biclustering analysis of expression data.
Wu CJ, Kasif S.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W596-9.

CGI – Prioritize Genes by Integrating Expression data and Protein Interaction data

CGI

:: DESCRIPTION

CGI (Combining Gene expression and protein Interaction data) is intended to implement a new approach to prioritize genes by integrating expression data and protein interaction data.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CGI

:: MORE INFORMATION

Citation

Ma XT, Lee HJ, Wang L, and Sun FZ
CGI: a new approach for prioritizing genes by Combining Gene expression and protein-protein Interaction data
Bioinformatics (2007) 23 (2): 215-221.

CurveSOM – Curve-based Custering of Time Course Expression data

CurveSOM

:: DESCRIPTION

CurveSOM is a new clustering algorithm of curve-based custering of time course expression data . It first present each gene by a cubic smoothing spline that is fitted to its time course expression data and then group genes into clusters by applying a self-organizing map-based clustering on the resulting splines. CurveSOM is a very promising tool for the exploratory analysis of time course expression data, as it is not only able to group genes into clusters with high accuracy but also able to find true time-shifted correlations of expression patterns between clusters.

::DEVELOPER

Chen Xin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CurveSOM

:: MORE INFORMATION

Citation

X. Chen.
Curve-based clustering of time course gene expression data using self-organizing maps.
Journal of Bioinformatics and Computational Biology, vol. 7, no. 4, 645-661, 2009..

GaneSh – Cluster Expression Data by Gibbs sampling procedure

GaneSh

:: DESCRIPTION

GaneSh is a software to cluster expression data by Gibbs sampling procedure

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 GaneSh

:: MORE INFORMATION

Citation:

Joshi, A., Van de Peer, Y., Michoel, T. (2008)
Analysis of a Gibbs sampler method for model based clustering of gene expression data.
Bioinformatics 24, 176-83.