Microarray Analysis Resources

Databases

General databases

	GEO (NCBI}
	ArrayExpress (EBI)
	CIBEX (DDBJ)
	SMD (Stanford)
	GeneVestigator, expression of genes across tissues, conditions, and organisms.
	L2L MDB, The L2L Microarray Database, a collection of published microarray data.

Special databases

	GNF SymAtlas (Novartis)
	GeneNote (human)
	HuGE Index (human)
	READ - Riken Expression Array Database ( mouse)
	yMGV - Yeast Microarray Global Viewer (yeast)
	VirtualPlant

Expression databases, not necessarily microarrays

	SOURCE (Stanford)
	DDD (UniGene)
	BodyMap (human, mouse)
	SAGE (CGAP, NCI)
	Gene expression in rodents (MGI)
	Allen Brain Atlas (mouse)

Analysis Tools

General tools

	Affymetrix® Expression Console™ Software
	GeneChip-compatible™ Software Solutions Catalog
	Affymetrix software
	Affymetrix Tools
	Expression Profiler (EBI)
	Eisen Lab Software
	TM4 (TIGR)
	Expander (Ron Shamir's group)
	GenePublisher
	MicroArray Explorer
	BioConductor
	Genomics and Bioinformatics Group, Microarray Tools.
	ArrayQuest (free microarray analysis via the web, using R/Bioconductor and other)
	WebArray, Online Microarray Data Analysis Platform (based on R, Bioconductor, Limma)
	BRB Array Tools (NCI), an integrated package for the visualization and statistical analysis of DNA microarray gene expression data, with an Excel front end.
	INCLUSive web portal
	A list of public software (The Robert S. Boas Center for Genomics and Human Genetics)

Specific tools

	SNOMAD - Standardization and NOrmalization of MicroArray Data
	SAM: Significance Analysis of Microarrays
	FDR: False Discovery Rate
	dChip - DNA-Chip Analyzer. User Forum.
	maxd (maxdView)
	RMAExpress - Robust Multichip Average for Affymetrix arrays
	LIMMA - Linear Models for Microarray Data. For Windows: LimmaGUI (spotted), AffylmGUI (Affymetrix).
	STEM: Short Time-series Expression Miner
	Venn Diagram Generator
	Venny

ChIP-on-chip, Tiling Arrays

	MAT
	TAS and IGB (Affymetrix). Tutorial.
	CisGenome
	ChIPMonk

Visualization tools

Prism (paper in Bioinformatics)

Commercial tools

	GeneSpring (Quick start guide, tutorials, extras)
	SpotFire (tutorials)
	Partek

Probe identification tools

	GeneAnnot
	ADAPT
	XHM - cross hybridization on microarrays

Functional Annotation, GO tools

	NetAffx
	GOstat
	ChipInfo
	Onto-Express
	GenePublisher
	DAVID
	GARBAN
	GoMiner
	FatiGo - A web tool for finding significant associations of Gene Ontology terms with groups of genes. Uses: Search GO terms for this list of genes; compare two lists of genes and find GO terms differentially represented between them.
	GoToolBox - Performs functional investigation of groups of genes, based on the Gene Ontology^TM ressource.
	VirtualPlant
	GFINDer

Software using continuous evidence for differential expression, not predefined cutoffs:

	ErmineJ - Gene Ontology analysis for microarray data
	GSEA - Gene Set Enrichment Analysis

To find additional tools, simpley search PubMed with "Gene Ontology"[TI]

Pathway Analysis

	DAVID 2006
	PathwayExpress (Onto tools) - recommended
	GenMAPP, Gene Map Annotator and Pathway Profiler.
	Panther (Gene Ontology, pathways, SNPs)
	GoTM - recommended
	Reactome: PathFinder, SkyPainter
	Cytoscape

Motif/Promoter Analysis

	CONFAC - Conserved Transcription Factor Binding Site Finder
	TAMO - a tool which combines information from different programs for motif discovery, scoring, and analysis. In addition, the TAMO Package provides modules for integrating motif analysis with diverse data sources including genomic sequences, microarrays and various databases (Paper).
	FIRE, Finding Informative Regulatory Elements, by Noam Slonim (program not yet available)

Educational Sites - Statistics

	PROPHET Statistics Glossary
	Statistics with R

Educational Sites - Microarrays

	Affymetrix. Affymetrix learning center. Data analysis fundamentals.
	NCBI
	EBI
	The Scientist: The DNA Microarray
	GeneSifter: "The Seven Keys To Successful Microarray Data Analysis"
	Bibliography on Microarray Data Analysis
	Microarrays for Cancer Diagnosis and Classification (Book at NCBI)
	An (Opinionated) Guide to Microarray Data Analysis, Mark Reimers.
	A guidebook for DNA Microarray Data Analysis
	Limma: Linear Models for Microarray Data, Gordon K. Smyth. Chapter 23 from "Bioinformatics and Computational Biology Solutions Using R and BioConductor", Eds. R. Gentleman et al. Springer 2005.
	Very basic exercise on microarray analysis by Vered Caspi (link to data)

Additional Links

	Microarray resources (Stanford)
	Publications of microarray projects using Affymetrix technologies
	Gene-Arrays mailing list archive. Archive by thread.

Vered Caspi, Bioinformatics Support Unit, Ben-Gurion University of the Negev. Tel: 08-6479034