My Microarray Software Comparison - Data Mining Software (Comprehensive Software)


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Definition of data mining software - comprehensive software
Suggested readings
Data mining software - comprehensive software (in alphabetical order)

[ Acuity | AMIADA (Analyzing MIcroArray DAta) | ArrayStat | Avadis | BioMine | BRB ArrayTools | Cluster | DNA-arrays analysis tools | DNA-Chip Analyzer (dChip) | Engene | Expression Profiler | ExpressionSieve | GEDA | GeneLinker Gold | GeneLinker Platinum | GeneMaths | GenePattern | GeneSight | GeneSpring | Genesis | GeneWeaver | GeneXPress | GENOWIZARD | GEPAS | J-Express | MAExplorer | Partek software suites | Pathways 4 | ROSETTA | SilicoCyte | TIGR Multiple Experiment Viewer (MEV) | Vector Xpression NTI | XCluster | X-Miner ]


 

Definition of data mining software - comprehensive software

A comprehensive software incorporates many different analyses at different stages of microarray analysis like data preprocessing, dimensionality reduction, normalization, clustering and visualization in a single package.This type of software does not have any accompanied database although they are usually equipped with an interface for Open DataBase Connectivity (ODBC), a standard for accessing different database systems.

Suggested readings

    Experimental Design
  1. Glonek GF, Solomon PJ. Factorial and time course designs for cDNA microarray experiments. Biostatistics. 2004 Jan;5(1):89-111. [PubMed]
  2. Simon RM, Dobbin K. Experimental design of DNA microarray experiments. Biotechniques. 2003 Mar;Suppl:16-21 [PubMed]
  3. Kerr MK. Experimental design to make the most of microarray studies. Methods Mol Biol. 2003;224:137-47. [PubMed]
  4. Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet. 2002 Aug;3(8):579-588. [PubMed][full text][pdf][web supplement]
  5. Lee ML, Whitmore GA. Power and sample size for DNA microarray studies. Stat Med. 2002 Dec 15;21(23):3543-70. [PubMed]
  6. Hwang D, Schmitt WA, Stephanopoulos G, Stephanopoulos G. Determination of minimum sample size and discriminatory expression patterns in microarray data. Bioinformatics. 2002 Sep;18(9):1184-93. [PubMed]
  7. Simon R, Radmacher MD, Dobbin K. Design of studies using DNA microarrays. Genet Epidemiol. 2002 Jun;23(1):21-36. [PubMed]
  8. Kerr MK, Churchill GA. Experimental design for gene expression microarrays. Biostatistics. 2001 Jun;2(2):183-201. [PubMed]
    Data mining
  1. Leung YF, Cavalieri D. Fundamentals of cDNA microarray data analysis. Trends Genet. 2003 Nov;19(11):649-59. [PubMed]
  2. Smyth GK, Yang YH, Speed T. Statistical issues in cDNA microarray data analysis. Methods Mol Biol. 2003;224:111-36. [PubMed]
  3. Nadon R, Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends Genet. 2002 May;18(5):265-71. [PubMed]
  4. Sherlock G. Analysis of large-scale gene expression data. Brief Bioinform. 2001 Dec;2(4):350-62. [PubMed]
  5. Wu TD. Analysing gene expression data from DNA microarrays to identify candidate genes. J Pathol. 2001 Sep;195(1):53-65. [PubMed]
  6. Quackenbush J. Computational genetics computational analysis of microarray data. Nat Rev Genet. 2001 Jun;2(6):418-27. [PubMed][pdf]
  7. Brazma A, Vilo J. Gene expression data analysis. FEBS Lett. 2000 Aug 25;480(1):17-24. [PubMed]

Data mining software - comprehensive software (in alphabetical order)

 
Product Company/ Institute Interface/ Operating System Features Price Remarks
Acuity 2.0 Axon Instruments Windows 2000/XP client; Windows 2000 server
(recommended)		 various visualation tools; normalization, hierarchical, k-means, k-medians clustering with many different similarity metrics, SOM, PCA, gene shaving. Scripting engine for customizable analysis through VBScript, JavaScript or ActiveX objects store data in relational database US$4,000 (U.S.A. and Canada only)  Full integration with GenePix Pro 4
AMIADA (Analyzing MIcroArray DAta) Department of Biology;
University of Ottawa		 Windows 98/NT/2000 organizing, exploring, visualizing, and analyzing microarray data.It features an EXCEL-like user interface and performs data transformation, PCA, a variety of cluster analysis etc.  for visualizing expression profiles. free download;tutorial; reference [PubMed]
ArrayStat 1.0 Imaging Research Inc. Windows NT/2000 normalization, statistical confidence analysis, p values, standard errors, Q-Q plot no pricing information is available ppt presentation; overview of statistical inference
Avadis Strand Genomics Windows, Linux, Mac OS X, Solaris, Desktop and Client-Server data import from files and RDBMS, Affymetrix support, advanced visualization capabilities, dynamically linked views, probe-level analysis, normalization, differential expression analysis for variety of experiment designs, clustering (K-means, Hierarchical, PCA, Eigen-value, SOM, Randomwalk), classification and prediction (SVM, Decision Trees, Neural Networks, MVA), automated batched gene annotation, data filtering and scripting capabilities.
 Available on request -
BioConductor many Windows, MacOS, Linux/Unix; requires R-environment
 an open source software project with several goals. Main goals: providing infrastructure in terms of design and software for analysing genomic data, especially microarray data, some form of graphical user interface for selected libraries and a mechanism for linking together different groups with common goal GNU GPL (version 2 or later) current released packages; current developmental packages; contributed packages;  faq;Vignettes; Short Courses (very useful!); Research Talks;
BioMine
 Gene Network Science
 Windows  95/98/NT/2000
 data import, normalization and replicate-handling, with Affymetrix GeneChip data handling capabilities; various clustering and statistical inference tools; an Experiment Design Tool indicates how many replicates are needed to statistically validate features of interest in microarray data.
  $1000 (academic) per seat per year
$5000 (commercial) per seat per year
 description;datasheet;overview white paper;
BRB ArrayTools 3.1 Molecular Statistics and Bioinformatics Section, Biometric Research Branch, NCI Windows integrated package for the visualization and statistical analysis of DNA microarray gene expression data, normalization, scatterplot, clustering, multidimensional scaling, class prediction no pricing information is available download;technical reports and talks
Cluster Michael Eisen's lab;Lawrence Berkeley  National Lab (LBNL) Windows 95/98/NT hierarchial clustering, K means clustering
Self-Organizing Map (SOM), PCA		 Free for academic user download;manual; source code; demo data; reference [PubMed][pdf][web supplement]; also available from stanford university and microarray.org; the output is visualized by TreeView
DNA-arrays analysis tools National Spanish Cancer Center (CNIO) web a suite of web-based programs for DNA array data analysis including two sample correlation plot, hierarchial clustering, SOM, self organising hierarchical neural network (SOTA) and various tree viewers. Free -
DNA-Chip Analyzer (dChip) Wong Lab
Department of Statistics,
Harvard University		 Windows NT/2000 normalization, model-based expression, filtering and comparison,
clustering		 Free for academic user reference [PubMed][pdf]
Engene Computer Architecture Department, Universidad de Malaga Web
 a web-based and platform independent exploratory data analysis tool for gene expression data that aims at storing, visualizing and processing large sets of expression patterns
 Free access upon request
 user manual;training data; demo tour; Reference [PubMed]
Expression Profiler European Bioinformatics Institute EBI Unix-like httpd server, any web client clustering, analysis and visualization of gene expression and sequence data.  Free paper (link to journal)
ExpressionSieve BioSieve Java, tested on windows 2000, 98, NT, 95, ME, Linux linking 
biological significance to expression patterns, data and analysis process management, signature gene discovery and class discovery & prediction		 academic discount available Modular pricing available
Gene Expression Data Analysis Tool (GEDA)
 UPCI, Center for Pathology Informatics Web
 A free, open-source, collaborative online gene expression data analysis web application with a rich variety of normalization steps, tests for differentially expressed genes, and sample classification algorithms, with online recommendation for analysis based on extensive simulation results.
 Free
 Recommendations for Analysis
GeneLinker Gold 3.0 Molecular Mining Corporation Windows normalization, missing value estimation, filtering, hierarchical clustering, parititional clustering( k-means and mutual nearest neighbors(Jarvis-Patrick), SOMs, PCA, various distance metrics and visualization functions, Gene Lists for support of pathways, functional classifications & ontologies, links to external databases, hierarchical history of analysis procedures Commercial = $3,995 Academic = $2,495 FAQ;Demo upon registration;
Products and Services;
Literature;
GeneLinker Platinum 2.0
 Molecular Mining Corporation Windows Platinum offers all the features listed for GeneLinker Gold plus SLAM algorithm and supervised learning tools, IBIS (Integrated Bayesian Inference System) algorithm, Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA), and Uniform/Gaussian Discriminant Analysis (UGDA) classifiers for inferencing of rules that produce multigenic markers for disease and tox response and predict complex phenotypes and gene-gene interactions. Each prediction has an associated accuracy percentage and an MSE (mean squared error) value.
 Contact MMC Sales for pricing
 FAQ;Demo upon registration;
Products and Services;
Literature;
GeneMaths Applied Maths Windows hierarchial clustering, bootstrap analysis, dendrogram manipulating tools, Self-Organizing Map (SOM), PCA, etc; simple to use, very friendly GUI, fast clustering algorithms, powerful script language, import data from any source or database using ODBC. US$6200 Demo Available; brochures; interact with Media Cybernetics ArrayPro seamlessly.
GenePattern
 Broad Institute
 Windows, MacOS X, Linux/UNIX
 a flexible analysis environment, allows users to do the following, in addition to being a standard microarray analysis application: Chain analysis tasks into pipelines for reuse and reproducible research, Run analyses from a programming language (currently R),
Run completely standalone on a laptop or in client-server mode.
 Free; registration required
 Download; faq; tutorial; algorithms; datasets; mailing list
GeneSight BioDiscovery Windows 9x/ Nt4/ Win2k/ WinXP, Linux, Mac GenePie visualization, 2-D and 3-D scatter plots, interactive ratio histogram plotting, hierarchical and neural network clustering, PCA, and Time Series Analysis. Significance and confidence analysis.  Chromosome Viewer.  Annotation Collector. no pricing information is available demo upon registration; reference [PubMed]
GeneSpring 6.1
 Silicon Genetics
Windows; Mac; Linux
 Analyze various array types, scatter plot, cluster analysis, PCA, SOM, statistic tools, 2D, 3D plotting no pricing information is available Product tour; Online demo; trial upon registration; pdf data sheet; citations; reference (link to journal)
Genesis Bioinformatics Group, Institute of Biomedical Engineering, Graz University of Technology Java, tested on Windows 2000, LINUX, Thru64 UNIX, Solaris and Irix A Java suite containing various tools such as filters, normalization, visualization tools, common clustering algorithms, SOM, k-means, PCA, SVM, map gene onto chromosomal sequences Free for academic download;documentation;licensing; Reference [PubMed]
GeneWeaver Visual Bioinformatics Java run under Windows 2000; Oracle 8i a software and database solution for analysis of gene expression data in an integrated project management environment; can manage data derived from the major types of experimental methods, divided into sequencing-based (EST/SAGE) and hybridization-based (micro/macro arrays) methods.  no pricing information is available presentation;documentation; 
GeneXPress
 Stanford University
 Windows, Linux/Unix
 GeneXPress is a visualization and analysis tool for gene expression data, integrating clustering, gene annotation, and sequence information. GeneXPress allows you to load clustering results and automatically analyze them for significance of functional groups through correlation with functional annotations (e.g. Gene Ontology) and for enrichment of motif binding sites (e.g. TRANSFAC motifs).
 Free for academic
 download; tutorials; faq
GENOWIZARD Genotypic Technology
Windows/ Linux
 Visualization tools, normalization, reporting functions, excel like interface.
no pricing information is available
 brochure;
GEPAS (Gene Expression Pattern Analysis Suite)
Bioinformatics Unit; CNIO
 web
 A comprehesive online suite for data preprocessing; viewing; hierarchical clustering, SOTA, SOM, SOM-tree clustering; Pomelo tool for multiple testing for differential gene identification; SVM; Data Mining with Gene Ontology
 free
 Documentation;
J-Express 2.1 MolMine Java Hierarchical clustering, K-means particional clustering, Principal component anlaysis, Self-organizing maps, Profile similarity search, Normalization and filtering, Raw data import, Project organization Free for academics Download (registration required); plugins;screenshot; Old Version 1.0 (free for all users); Old version 1.0 Online tutorial
MAExplorer Open Source at the SourceForge  Java; either standalone or run as applet normalization methods, data filtering, scatter plots, histograms, expression profile plots, similar gene clustering, hierarchial clustering, K-means and K-median clustering, gene and sample sets, dynamic reports. Direct manipulation. Plugin facility for adding user analytic methods being alpha-tested. Data conversion wizard. Direct
access to other genomic databases.		 Mozilla Public License
1.1 (MPL 1.1)		 summary;documentation;manual;pdfs; tutorial;download;
very comprehensive online resources;
 
Partek software suites Partek UNIX, Linux, Windows 2000, NT, 98, 95 comprehensive processing, analysis, and visualization of data; Exploratory Data Analysis; Statistical Inference; Predictive Modeling; connectivity to third-party database, web, and software applications. no pricing information is available Screenshot;Demo Available
Pathways 4
 Invitrogen
 Windows, Linux/UNIX, MacOS X
 Visualization, filtering, statistical inference of differential expression, various clustering algorithms, extensible by plugins
 no pricing information is available -
ROSETTA
 Knowledge Systems Group, Dept. of Computer and Information Science, Norwegian University of Science and Technology
 Windows 2000/XP, Linux
 ROSETTA is a toolkit for analyzing tabular data within the framework of rough set theory. ROSETTA is designed to support the overall data mining and knowledge discovery process: From initial browsing and preprocessing of the data, via computation of minimal attribute sets and generation of if-then rules or descriptive patterns, to validation and analysis of the induced rules or patterns.
 Free?
source code is also available. Features; Download; Resources;
SilicoCyte CytoGenomics Inc
 Windows 2000/XP
 An integrated microarray analysis software and includes modules for Image Analysis, Data Annotation, Data Analysis,
Statistical Analysis
 US$999 for academic user
TIGR Multiple Experiment Viewer (MEV) The Institute of Genomic Research (TIGR) Windows, LINUX, UNIX, MacOS X Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes. Numerous normalization, clustering and distance algorithms have been implemented, along with a variety of graphical displays to  best present the results. MEV was written to be flexible and expandable, and supports a variety of input and output formats.  Free (Open Source
 User guide; Download Program; Download Program and Source; Reference [PubMed]
Vector Xpression 3.0 Informax Inc. Windows import, normalize, and merge primary expression run results obtained under a variety of experimental conditions. Filtering, sorting, clustering algorithms, profiling and plotting methods; Automation through recordable macros; Internal editor and functionality for R statistical and Matlab; Multiple Correction Techniques; Two Group Comparison; 3 or More Group Comparison
 following this link for pricing information
 Free trial after registration; demo video; brochure;
XCluster Stanford University Unix/ Linux/ Mac/ Windows A program similar to Cluster, perform hierarchical clustering, self-organizing maps Free for academic and nonprofit user -
X-Miner X-MINE client based server (Sun Solaris, Linux) or Web. an integrated suite of Supervised (tree harvesting series (Classifier, Isolator, Quantifier, Survivor) and the Sam Series
(X-Sam Q., X-SamIso., X-SamSurv. X-SamPair) /Unsupervised (hierarchical clustering, SOM, K-Mean, K-Medioid, PCA, and  X-Shaving) analytics for microarray data. The platform has four filtering options available for cDNA and affy data, three normalization options and three data imputation options. 		 no pricing information is available Demo available;

last updated: 15 Jan 2004
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