MIAME List of MD Software Microarray Software Comparison

Microarray Software and Databases Software Category Description SMD Database Stanford LonghornArray Database Database OK State U YaleMicroarray Database Database Yale AMAD Database microarrays.org ArrayExpress Database EBI caArray Database NCI MicroarrayEXP Database USDA - Soybean Gene ExpressionOmnibus Database NCBI UNC Microarray Database Database Univ of N Carolina - Chapel Hill MaxD Database Manchester Bioinformatics NOMAD Database Chris Seidel's Lab MIDAS Database Sanger IMAD Database Illinois BASE Database Lund University QuickLIMS Database MS Access version DAVID annotation Provides a comprehensive set of tools forinvestigators to visually summarize annotation from large list ofgenes. dragonhopkins annotation Geneannotation tool geneLynx annotation Geneannotation genetide annotation Geneannotation globalviewer annotation providesa synthetic view of the transcriptional expressionprofiles of yeast genes karma annotation Arraymanager and annotator matchminer annotation nablesthe user to translate between disparate ids for the same gene netaffyx annotation Affymetrixtools for annotation Panther annotation Geneannotation RESOURCERER:(TIGR) annotation provides annotation based on the TIGR GeneIndices (TGI) R SOURCE annotation CDFfiles array information Microarrays Data Libraries chipinfo array information CloneTracker arrayinformation System for managing and processing allinformation associated with fabrication of spotted microarrays ArrayMaker array maker provideshigh performance robotic control of microarrayer robots eXPatGen cluster analysis AnOn-line Gene Expression Pattern Generator Clusteranalysis clusteranalysis On line software that do unsupervisedClustering CWTC clusteranalysis A method designed to mine large sets ofmicroarray data. The basic idea is to perform two kinds of clusteranalysis; fcluster clusteranalysis Software for fuzzy clustering FreeView clusteranalysis Agene dendrogram viewer FuzzyClustering clusteranalysis Containswell-known algorithms like the fuzzy c-means algorithm GHMM cluster analysis MaxPlanck Institute for Molecular Genetics, Department of ComputationalMolecular Biology, University of Cologne GIMM cluster analysis A clustering procedure based on theconcept of Bayesian model-averaging and a precise statistical model ofexpression data GQL clusteranalysis A GHMM-based tool for querying andclustering Gene-Expression time-course data) HeatMapBuilder clusteranalysis Generates customizable heatmaps frommicroarray data lexcavator cluster analysis asoftware tool used for gene expression data clustering.EXCAVATOR can run on any platform with the Unix or Linux operatingsystem. MCVE clusteranalysis A cluster validity tool for geneexpression data page cluster analysis Tool to attach expression pattern to genesrepresented in a collection of hybridization array experiments QuantumClustering cluster analysis SOTA clusteranalysis On line software that do Clustering(calculus and graphics) svmlight clusteranalysis This software does SVM (Clustering) TreeArrangeand Treeps clusteranalysis Tool for displaying expression array dataand optional associated heirarchial clustering in the form ofencapsulated postscript files TreeView clusteranalysis Graphically browse results of clusteringand other analyses from Cluster XCluster clusteranalysis Perform hierarchical clustering,self-organizing maps expressionanalysis custom analysis Specializinginmicroarray analysis,bioinformatics, and expression gene profiling service. MicroarrayData Assembler data assmebly Excel-basedsoftware developed by Anbazhagan Ramaswamy forassembling microarray data biogopher data integration facilitatesthe integration of your local bioinformatics data with public datasources MAPS data integration System for management and interpretationof microarray gene expression experiment information and data Microhelper data integration for merging datasets, checking dataintegrity, filtering noises, and normalizing data ondex data integration Enables data from diverse biological data sets to be linked, integrated andvisualised ACID database adatabase for microarray clone information BASE database A comprehensive database server to managethe massive amounts of data generated by microarray analysis. gominer gene ontology atool for biological interpretation of 'omic' data GO-TermFinder gene ontology Finds GO terms significantly associatedwith a list of genes OntologyTraverser gene ontology GOsearch using R SparseLOGREG gene selection It makes use of LTI-Lib and the PythonImaging Library. I AbleImage Analyser image analysis supports image analysis functions thatinclude dimensional, gray scale and 24 bits color measurements. ArrayFox image analysis Automatic detection of background noiseand contaminations. Array-Pro image analysis A tool for the nascent microarray andhigh-throughput screening research efforts fueling the genomics,proteomics, drug discovery and bioinfor ArrayVision image analysis A flexible software package for thequantification of gene expression and protein arrays. Dapple image analysis A program for quantitating spots on atwo-color DNA microarray image. GenePixPro image analysis Batch Analysis tab for browsing andanalyzing batches of images GridGrinder image analysis Offers industrial strength image analysisfeatures for microarrays Iconoclust image analysis A powerfulimaging software for the analysis of array images of multipleformats. ImaGene image analysis imageanalysis Koadarray image analysis imageanalysis MACROview image analysis Analyzes microarray images in TIFF formatthat are generated by microarray scanners MicroVigene image analysis Includes many features and functions thatwill facilitatemicroarray images. MicroVigene image analysis imageanalysis PhoretixArray image analysis imageanalysis QuantArray image analysis imageanalysis ScanAlyze image analysis imageanalysis SensiChipView image analysis An image analysis software package focusedto allow streamlined and intuitive image and data evaluation andproceding Spatter:(Savannah) image analysis A software package which performs DNAmicroarray image analysis.er, and does not require any user interactionwhile it runs. Spot image analysis imageanalysis SpotReader image analysis imageanalysis Cytoscape network visualization Visualizemolecular interaction Pajek:Large Network Analysis network visualization   Relnet network visualization constructrelevance networks from their gene expression data. Arrayplot normalization Normalisation software, with somevisalisation tools SNOMAD normalization Standardization and Normalization of MicroArray Data BAGEL pathwayanalysis BayesianAnalysis of Gene Expression Levels: a program for the statisticalanalysis of spotted microarray data. GenMAPP pathwayanalysis Tools for visualizing data from geneexpression experiments in the context of biological pathways. MGraph pathway analysis Graphicalmodels for microarray data analysis ArrayDesigner primer design Tool assisting in primer design formicroarray construction arrayExpress repository publicrepository for microarray data princetondb repository ArrayStat statistical package A unique statistical package that has beendesigned for analysis of microarray gene expression data BAGEL statisticalpackage Bayesian Analysis of Gene ExpressionLevels: a program for the statistical analysis of spotted microarraydata. BAMarray statisticalpackage Bayesian Analysis of Variance forMicroarrays - detect differentially expressed genes from multigroupmicroarray data ChipST2C statisticalpackage HCA, K-means cluster analysis, T-test,Mann-Whitney, F-test, Kruskal-Wallis, Significant genes listed in Excelspreadsheets. CLUSFAVOR statisticalpackage unsupervised hierarchical cluster andprincipal component analyses of DNA microarray transcriptional profiles. CyberT statisticalpackage t-test for statistically significantdifferences between sample sets for arrays; DTREG statisticalpackage Apowerful statistical analysis program GeneMaths statistical package tools fortime-course experiments GLR statisticalpackage A statistical analysis program toidentifydifferentially expressed genes from microarray data. iGEA statistical package Foruse from the Windows command line KNNimpute statisticalpackage Estimation of missing microarray values MA-ANOVA statistical package A set of functions written in Matlab forthe analysis of variance on microarray data. Octave statistical package Dataanalysis PAM statisticalpackage Prediction Analysis for Microarrays pcatutorial statistical package P-scan statistical package Peak Quantification using StatisticalComparitive Analysis R statisticalpackage A very popular software for statistician. SAM statistical package Significance Analysis of Microarrays :Supervised learning software for genomic expression data mining SAS statistical package statisticalanalysis Statistica statistical package statisticalanalysis SuperPC statisticalpackage Survival and regression analysis formicroarrays VERA& SAM statisticalpackage Finding significant expression differencesin DNA microarray data AMIADA suite an integrated computer program fororganizing, exploring, visualizing, and analyzing microarray data ANOVATool suite NIAArray Analysis tool AppliedMaths suite software ArrayMiner® suite A set of analysis tools using advancedalgorithms to reveal the true structure of your microarray data. ArrayPack suite Offers a suite of applications whichmanages all three parts of array expression projects. arraypipe suite A Flexible Processing Pipeline for Microarray Data arraytrack suite Microarraysuite BioConductor suite An open source software for analyzinggenomic data,especially microarray data BioDiscovery suite Image analysis, data management and tracking and data analysis software(Windows 95/98/NT4). BRBarray tools suite An integrated package for thevisualization and statistical analysis of microarray gene expressiondata. T CAGED suite Based on amethod called Bayesian Clustering by Dynamics, cageda suite A free, open-source, collaborative onlinegene expression data analysis web application DAMA suite Microarrayservice dChip suite Low-level and high-level analysis ofoligonucleotide microarrays EBItools suite microarraytool collection engene suite Analysis tools for visualizing, pre-processing and clustering microarrayexpression data Enodar suite Vendor expressyourself suite Microarraydata processing platform ExpressionProfiler suite A set oftools for clustering, analysis and visualization of gene expression andother genomic data. T sequences, study protein interactions, as well asto link analysis results to external tools and databases. Expressionist suite Analysistools ExpressionSieve suite Microarray data analysis package, strongin linking biological significance to expression patterns, GAAS suite An integrated software framework forefficient management, analysis and visualization of large amounts ofgene expression data GCOS suite Microarray suite GEDA suite GeneExpression Data Analysis Tool genepattern suite Supervised classification, gene selectionand permutation test methods. genepublisher suite performsautomated data analysis GeneSifter suite Combines data management and analysis tools. GeneDirector suite acomprehensive microarray data management solution geneGobi suite exploratoryanalysis of microarray data and metabolic networks GeneLinker suite Gene expression and proteomics analysis software. GenePattern suite apowerful analysis workflow tool GenePilot suite Apowerful and intuitive MicroArray Analysis tool GenePublisher suite Perform automated data analysis from geneexpression experiments on a number of different platforms. GeneSifter suite Access to powerful statistical toolsthrough a web interface, with integrated features for determining thebiological significance of the data. GeneSight suite Microarray suite Genesis suite Microarraysuite GeneSpring suite An analytical workbench for microarraydata analysis that enables visualization, organization and manipulationof gene expression data GeneX suite a client application that provides aninterface to a relational database managment system GeneXplorer suite Gene Expression Database : integratedtoolset for data analysis and comparison GeneXPress suite Microarraysuite GenMaths suite Analysis of high density microarrays andgene chips Genowiz™ suite A Gene Expression Data Analysis andManagement Tool. GEPAS suite A collection of tools for complete dataanalysis GEPS suite provides interactive pattern analysis gfinder suite Genome Function INtegrated Discoverer GSEA suite Gene set enrichment analysis IBMgene works suite a softwarepackage toanalyze patterns in gene array chip data. INCLUSive suite INCLUSive(INtegrated CLustering, Upstream Sequence retrieval and motif) J-ExpressPro: (MolMine) suite a comprehensive portable software package LACK suite Charles C Kim & Stanley Falkow,Stanford University limma suite ABioconductor module MAExplorer suite Analyzed microarray data in specific steps. Matarray suite aset of Matlab tools designed for the analysis of microarray data. matlabtoolbox suite providesseveral methods for analysis mchips suite integratedwith a software platform for microarray data analysis MIDAS suite Dataanalysis NIAMicroarray ANOVA Tool suite Dataanalysis OntoTools suite Softwaresuite orangecanvas suite Partek suite PARTISANarrayLIMS suite RACE suite Rosetta suite Arraymanager and annotator ScoreGenes suite SeqExpress suite SilicoCyte suite An advanced, modular, flexible and highlyintegrated microarray analysis platform SMD suite Microarray suite SpotfirePro suite Spotfire Pro from Spotfire, Inc. STEM suite AJava program for clustering, comparing,and visualizing short time series gene expression data ( SVDMAN suite Program for Singular Value DecompositionAnalysis of global gene expression data TableView suite Center for Computational GenomicsandBioinformatics, University of Minnesota THEA suite suite TIAMD suite Microarray suite Vampire suite Microarray suite VextorXpression suite Normalization, Filtering, sorting,clustering algorithms CaryoScope visualization Viewing aCGH or expression data in awhole-genome context. ciMiner visualization generatescolor-coded Clustered Image Maps to representgene expression profiles Cleaver1.0 visualization Provides a variety of tools to assist inthe analysis of microarray expression data. I Cluster visualization FromEisen’s lab Cluster3.0 visualization Perform hierarchical clustering,self-organizing maps F-scan visualization F-scan For the two channels of an image,generate a file containing spot intensities and addresses and display ascatterplot. Compare spot intensities between the red and greenchannels and generate a list of over and under expressed genes.Visually examine pairs of spots reported as differentially expressed. JavaTreeview visualization View Results of Clustering OmniViz visualization Datavisulaization pcasvd visualization slcview visualization ViewResults of Clustering VennMapper visualization Smid M, Dorssers LC, Jenster G.Departmentof Pathology, Josephine Nefkens Institute. The Netherlands.

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