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GeneXplorer specifications


Unique identifier OMICS_24241
Name GeneXplorer
Alternative name Microarray-GeneXplorer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A set of frames that can be used for viewing the expression data.
Output format HTML
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Version 0.11
Stability Stable
Maintained Yes




No version available


  • person_outline Gavin Sherlock
  • person_outline Christian Rees
  • person_outline Janos Demeter
  • person_outline John Matese
  • person_outline David Botstein

Publication for GeneXplorer

GeneXplorer citations


The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach

PMCID: 4758378
PMID: 26949515
DOI: 10.5256/f1000research.6818.r9713

[…] nteractive inspection of expression of UPR genes across the integrated experiments, we implemented the UPR-HD tool. It is database with a web-interface based on a modified and enhanced version of the GeneXplorer software . UPR-HD enables the query of individual or multiple UPR genes, the visualization of the expression changes observed in the microarray experiments and their export in table format […]


Toward a systems level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

Front Genet
PMCID: 4079066
PMID: 25071821
DOI: 10.3389/fgene.2014.00191

[…] ies for 3073 genes. It aims to assist researchers in the characterization and functional annotation of genes using the guilty-by-association principle. Its visualization tool is a modified version of GeneXplorer (Rees et al., ). Different data subsets can be selected, with genes associated to different functions, based on whether all perturbations (genetic and environmental) or only environmental […]


CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803

PMCID: 3400984
PMID: 22829745
DOI: 10.6026/97320630008634

[…] f genes was obtained from Cyanobase []. The clustered expression matrices can be visualized and queried through a Common Gateway Interface (CGI)-based application, which is a modified version of the GeneXplorer software []. CyanoEXpress is currently running on an Apache web server under an Ubuntu Linux operating system.Expression data for all genes, but only for perturbations of environmental con […]


CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data

PLoS One
PMCID: 3236239
PMID: 22174941
DOI: 10.1371/journal.pone.0028990

[…] conductor (, Chipster ( , CLC Genomics Workbench (CLC bio), Expression Profiler (European Bioinformatics Institute) , GeneSifter (PerkinElmer, geospiza) , GeneXplorer (Stanford University) , GeneSpring (Agilent Technologies), J-Express ( , Mayday ( , Mayday SeaSight , PartekĀ® Genomics […]


Visualization methods for statistical analysis of microarray clusters

BMC Bioinformatics
PMCID: 1156867
PMID: 15890080
DOI: 10.1186/1471-2105-6-115

[…] eMap [] provides an innovative way to visualize hierarchically clustered data as well as data organized in the context of the GO hierarchy, but is not intended for cluster analysis. New tools such as GeneXplorer [] provide an interactive method for visualization and analysis of microarray data on websites, but do not focus on the task of cluster analysis. Several tools, including the MultiExperime […]


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GeneXplorer institution(s)
Department of Genetics, Stanford University Medical School, Stanford, CA, USA; Department. of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Lewis-Sigler Institute for Integrative Genomics Carl Icahn Laboratory, Princeton University, Princeton, NJ, USA
GeneXplorer funding source(s)
Supported by a grant from the NHGRI, R01HG002732.

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