Microarray, SAGE and other gene expression data analysis tools

OBRC

	AMIC@ -- All MIcroarray Clusterings @ once
	A light-weight multi-method clustering engine for microarray gene-expression data.

	ASIAN -- a web server for inferring a regulatory network framework from gene expression profiles
	Infer a framework of regulatory networks from a large number of gene expression profiles.

	ActionMap -- a web-based software that automates loci assignments to framework maps
	Perform automated genetic mapping on a fixed framework map.

	AffyGCQC -- Affymetrix GeneChip Quality Control
	A web-based interface to detect outlying genechips with extreme studentized deviate tests.

	AffyMAPSDetector -- Affymetrix MicroArray Probe SNP Detector
	A software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.

	Applications for protein sequence–function evolution data -- mRNA/protein expression analysis and coding SNP scoring tools
	Conduct protein classification, expression analysis and SNP function screening.

	Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis
	Identify co-expressed genes based on n a large Arabidopsis thaliana microarray data set.

	ArrayPipe -- A Flexible Processing Pipeline for Microarray Data
	Automatically apply of complex analyses to microarray data ranging from single slides to large data sets including replicates and dye-swaps.

	ArrayProspector -- A Web Resource of Functional Associations Inferred from Microarray Expression Data
	Predict functional associations between genes based on microarray expression data.

	ArrayQuest -- a web resource for the analysis of DNA microarray data
	Use a web-based Linux platform to implement DNA microarray data analysis programs.

	ArrayXPath -- Mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
	Map and visualize microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG).

	Asterias -- Integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
	Analyze gene expression and aCGH data.

	BABELOMICS -- advanced functional profiling of transcriptomics, proteomics and genomics experiments
	Suite of web tools for the functional profiling of genome scale experiments.

	BTW -- a web server for Boltzmann time warping of gene expression time series
	Compare temporal gene expression pattern from different samples.

	BiVisu -- Bicluster Visualization
	Software tool for bicluster detection and visualization.

	BicOverlapper -- a tool for bicluster visualization
	A visualization technique to simultaneously represent all biclusters.

	CARMAweb -- comprehensive R- and bioconductor-based web service for microarray data analysis
	Perform comprehensive analysis of microarray data.

	CARRIE -- Computational Ascertainment of Regulatory Relationships Inferred from Expression
	Analyze microarray and promoter data to infer transcriptional regulatory network.

	CONFAC -- Automated application of comparative genomic promoter analysis to DNA microarray datasets
	Find the conserved Transcription Factor Binding Sites (TFBS) in the promoter regions of the genes of given Human genes and the corresponding Mouse homolog.

	CRSD -- a comprehensive web server for composite regulatory signature discovery
	Conduct multi-facet analysis of composite regulatory signature by transcription factors and microRNA on gene expression.

	ChipInfo -- software for extracting gene annotation and gene ontology information for microarray analysis
	Retrieve annotation information from online databases such as NetAffx and Gene Ontology and organizing such information into easily interpretable tabular format outputs.

	Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription
	Perform automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles.

	DEEP -- Differential Expression Effector Prediction
	A tool that takes your data on differential gene expression (i.e. SAGE or microarray data) and predicts additional molecules which may be of importance.

	DetectiV -- Analysis of pathogen detection microarray data
	Visualization, normalization and significance testing for pathogen-detection microarray data.

	ECgene -- Genome annotation for alternative splicing
	Search for annotated information about gene structure, function and expression, and alternative splicing events.

	ESTAnnotator -- a tool for high throughput EST annotation
	Perform high throughput annotation of expressed sequence tags (ESTs).

	ESTpass -- a web-based server for processing and annotating expressed sequence tag (EST) sequences
	Clean and annotate expressed sequence tag (EST) sequences.

	Eu.Gene Analyzer -- a tool for integrating gene expression data with pathway databases
	An easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways.

	ExpressYourself -- a modular platform for processing and visualizing microarray data
	Use this fully integrated platform for processing microarray data.

	Expression Profiler -- An online platform for analysis of microarray data
	Analyze microarray gene expression and other functional genomics-related data.

	FFPred -- feature-based function prediction
	An integrated feature-based function prediction server for vertebrate proteomes.

	FatiGO -- a web tool for finding significant associations of Gene Ontology terms with groups of genes.
	Search for gene ontology (GO) terms for a list of genes.

	FatiGO+ -- a functional profiling tool for genomic data
	Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

	GAzer -- Gene Set Analyzer
	A web-based integrated gene set analysis tool covering previously reported parametric and non-parametric models.

	GBA server -- EST-based digital gene expression profiling.
	Perform EST-based gene expression profiling and analysis.

	GEDI -- Gene Expression Data Interpreter
	A user-friendly toolbox for analysis of large-scale gene expression data.

	GEMS -- a web server for biclustering analysis of expression data
	Perform biclustering of microarray data.

	GEPAS -- gene expression pattern analysis suite
	Conduct comprehensive analysis of microarray data.

	GEPS -- the Gene Expression Pattern Scanner
	Analyze gene expression patterns from microarray data.

	GOAL -- Automated Gene Ontology analysis of expression profiles
	Identify functions and processes regulated in microarray and SAGE experiments.

	GOEAST -- Gene Ontology Enrichment Analysis Software Toolkit
	A web-based software toolkit for Gene Ontology enrichment analysis.

	GenMAPP--Gene Microarray Pathway Profiler
	Visualize and analyze gene expression data in the context of biological pathways.

	GeneCruiser -- a web service for the annotation of microarray data
	Annotate microarray data using information from public databases.

	GenePublisher -- automated analysis of DNA microarray data
	Perform automated data analysis from gene expression experiments on a number of different platforms.

	GeneTrail -- advanced gene set enrichment analysis
	Analyze a set of genes against any chosen reference set or against all genes.

	GeneXPress
	To visualize and analyze gene expression data, and integrate clustering, gene annotation, and sequence information.

	INCLUSive -- a web portal and service registry for microarray and regulatory sequence analysis
	Use a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

	ISACGH -- InSilicoArray CGH
	A web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.

	Iccare -- Merge Sequence and Mapping Information for Plant and Animal Species
	Annotate crude EST (expressed sequence tag) specifically dedicated to comparative mapping approaches.

	JProGO -- a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information
	Analyze and interpret high-throughput gene expression data from prokaryotes.

	KARMA -- Compare and Annotate Heterogeneous Microarray Platforms
	Compare and annotate user-defined pairs of microarray platforms based on diverse types of genome annotation data (across different species) collected from multiple sources.

	M-BISON -- microarray-based integration of data sources using networks
	Identify differentially expressed genes.

	M@IA -- a microarray integrated application
	A modular open-source application for microarray workflow and integrative datamining.

	MA2C -- Model-based analysis of two-color arrays
	A novel normalization method based on the GC content of probes for two-color tiling arrays.

	MADNet -- MicroArray Database Network
	Data mining and visualization tool for rapid analysis of diverse high-throughput biological data.

	MAGMA -- analysis of two-channel microarrays made easy
	Identify differentially expressed genes from two-channel microarray data.

	MAPPFinder
	To create a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP.

	MAnGO -- Microarray Analysis at the Gif/Orsay platform
	An interactive R-based tool for two-colour microarray analysis.

	MD-SeeGH -- a platform for integrative analysis of multi-dimensional genomic data
	Allows users to rapidly and directly analyze genomic datasets spanning multiple genomic experiments.

	MIDAW -- a web tool for statistical analysis of microarray data
	Conduct statistical analysis to microarray data.

	MaRe -- Microarray Retriever
	A web-based tool for searching and large scale retrieval of public microarray data.

	NCBI GEO -- Mining millions of expression profiles—database and tools
	Search, submit, and store high-throughput gene expression data.

	OREST -- the online resource for EST analysis
	Analyze large amounts of ESTs or cDNAs from mammalia and fungi.

	OSCAR -- Open System for Cluster Analysis of Microarray Data
	Web platform for cluster and cross-species analysis of microarray data.

	Onto-CC -- Gene Ontology Conceptual Clustering
	A web server for identifying Gene Ontology conceptual clusters.

	Onto-Tools -- an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
	Use a suite of tools to analyze microarray data and perform genomic and proteomic annotations.

	PRISM -- Genomic data visualization on the Web
	Visualize microarray data via heat maps.

	PathExpress -- a web-based tool to identify relevant pathways in gene expression data
	Interpret gene expression data obtained from microarray experiments.

	PathwayExplorer -- web service for visualizing high-throughput expression data on biological pathways
	Visualize high-throughput microarray gene expression data on biological pathways.

	ProfCom -- profiling of complex functionality
	A web tool for profiling the complex functionality of gene groups identified from high-throughput data.

	RACE -- Remote Analysis Computation for gene Expression data
	Analyze DNA microarray data.

	REDUCE -- an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
	Use motif-based regression method to analyze microarray data.

	SAGE Anatomic Viewer (SAV)
	Find relative expression of a given gene in normal and malignant tissues throughout the human body.

	SAGExplore -- a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation
	Map experimental tags in serial analysis of gene expression.

	T-STAG -- resource and web-interface for tissue-specific transcripts and genes
	Analyze tissue/tumor-specific expression patterns in human and mouse transcriptomes.

	T-profiler -- scoring the activity of predefined groups of genes using gene expression data
	Use the t-test to score changes in the average gene expression activity of predefined groups of genes.

	TRANSPATH ® -- An integrated database on signal transduction and a tool for array analysis
	Analyze and visualize gene regulatory networks that combines encyclopedic information on signal transduction pathway.

	The Stanford Microarray Database -- Data access and quality assessment tools
	Search for raw and normalized data from microarray experiments, as well as their corresponding image files.

	VAMPIRE microarray suite -- a web-based platform for the interpretation of gene expression data
	Interpret microarray gene expression data.

	VIRGO -- computational prediction of gene functions
	Predict gene function using gene expression data.

	VistaClara -- An expression browser plug-in for Cytoscape
	A visualization plugin using an extended permutation matrix for exploratory data analysis of multi-experiment microarray studies.

	WEBSAGE -- a web tool for visual analysis of differentially expressed human SAGE tags
	Perform statistical analysis on human SAGE data.

	WebGestalt -- an integrated system for exploring gene sets in various biological contexts
	Search and analyze comprehensive genetic information of a set of genes.

	bioNMF -- nonnegative matrix factorization
	Reveal information about the complex latent relationships in experimental data sets.

	yMGV -- A Cross-Species Expression Data Mining Tool
	Identify the conditions that affect the expression of a gene or list of genes of yeast regulated in a set of experiments.