Bioinformatics Links Directory : Microarrays

This section contains links to microarray methods, standards for microarray data, and analysis tools for expression data.

WebGestalt - (Found July 2, 2008 )

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.
http://genereg.ornl.gov/webgestalt/

MIAMExpress - (Found July 2, 2008 )

MIAME (minimum information about a microarray experiment) compliant microarray data submission tool.
http://www.ebi.ac.uk/microarray/MIAMExpress/miamexpress.html

MedMiner - (Found July 2, 2008 )

MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also be done independently of a microarray gene set. Results are grouped based on a set of relational keywords.
http://discover.nci.nih.gov/textmining/

MatchMiner - (Found July 2, 2008 )

MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references.
http://discover.nci.nih.gov/matchminer/

MAGMA - (Found July 2, 2008 )

MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.
http://www.magma-fgcz.unizh.ch/pages/loginuser.jsf

KARMA - (Found July 2, 2008 )

KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID andor Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.
http://biryani.med.yale.edu/karma/cgi-bin/mysql/karma.pl

JProGO - (Found July 2, 2008 )

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
http://www.jprogo.de/index.jsp

ISACGH - (Found July 2, 2008 )

ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data andor expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.
http://isacgh.bioinfo.cipf.es/

GridGrinder - (Found July 2, 2008 )

Software for microarray image analysis.
http://gridgrinder.sourceforge.net/

GoSurfer - (Found July 2, 2008 )

GoSurfer is a tool for visualizing and comparing gene sets by mapping them onto Gene Ontology (GO) information in the form of a hierarchical tree. It is useful for investigating the results of microarray analyses or genome-wide computations.
http://www.biostat.harvard.edu/complab/gosurfer/