GeneX Va: VBC open source microarray database and analysis software

Abstract

Developed by the Virginia Bioinformatics Consortium (VBC), GeneX Va is an open source, freeware database and bioinformatics analysis software for archiving and analyzing Affymetrix GeneChip data. It provides an integrated framework for management, documentation, and analysis of microarray experiments and data to support a range of users, from individual research laboratories to institutional microarray facilities. GeneX Va also provides web-based access to a PostgreSQL relational database system with a comprehensive security system. Data can be extracted from the database and delivered to interactive or scriptable statistical analysis protocols. The security system allows each investigator to manage their own array data and analysis output files and also provides custom access privileges for other users, groups, and internal/external collaborators. The analysis interface uses "Analysis Trees," an innovative user interface that allows researchers to interactively create a tree-structured flow chart of analysis routines. The latest GeneX Va software is available from and can be freely downloaded at the Sourceforge web site http://va-genex.sourceforge.net. To allow researchers to access the database and analysis capabilities of the GeneX Va system, microarray data from many VBC GeneChip experiments have been deposited into a public section of the GeneX Va system at the University of Virginia. The VBC GeneX Va sites, which include documentation, are at http://genes.med.virginia.edu/ of the University of Virginia and at http://genex.csbc.vcu.edu/ of the Virginia Commonwealth University.

A-MADMAN: Annotation-based microarray data meta-analysis tool

“…Several software and web tools have been proposed for retrieval, organization and meta-analysis of microarray expression data from public repositories [ 13 - 21 ]. However, none of them offers the possibility to retrieve and organize both data and meta-information, to use the latter to re-annotate samples, and integrate data obtained from different platforms.…”

“…Different computational tools have been proposed for retrieval and meta-analysis of microarray expression data [ 13 - 21 ]. In particular, GEOSS (formerly GeneX) is a web-interfaced system for the storage and local analysis of microarray data [ 13 ]; CrossChip uses probe by probe sequence comparison to integrate data from different generations of Affymetrix arrays [ 14 ]; the server version of SeqExpress has a GEO integration tool which allows for retrieval and analysis of GEO Data Sets and GEO Series [ 15 ]; GenePattern contains a module ( GEOImporter ) for importing single GEO Data Sets or Series [ 16 ]; WGAS is a multi-purpose web-based analysis system [ 17 ]; GEOquery is a Bioconductor package for downloading and parsing SOFT files from GEO [ 18 ]; EzArray, is an Affymetrix-centered analysis system [ 19 ]; Microarray Retriever (MaRe) allows batch retrieval of microarray data from GEO and ArrayExpress according to user-defined searching criteria [ 20 ]; EMAAS allows importing and analyzing data from several repositories including GEO [ 21 ]. Some of these tools provide a user friendly interface for searching and retrieval of data from GEO and ArrayExpress, others implement database structures for storing and locally organizing the data and others offer modules for applying well established meta-analysis algorithms and procedures.…”

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

“…Amongst the gene expression profiling LIMS that have been reported [ 24 - 34 ], glass dual channel Cy5/Cy3 and oligonucleotide chips are extremely well catered for. However, Nylon based microarrays are at best marginally supported by these software, with more substantial Nylon support only to be found in commercial products[ 35 ].…”