My Microarray Software Comparison - Data Mining Software (Turnkey/Enterprise System)


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Definition of data mining software - Turnkey/Enterprise system
Suggested readings
Data mining software - Turnkey/Enterprise system (in alphabetical order)

[ arraySCOUT | BASE (BioArray Software Environment) | Expressionist | GAAS (Gene Array Analyzer Software) | Genedirector | GeneSifter.Net | Genetraffic | Genowiz | Rosetta Resolver | SilicoCyte | Silicon Genetics Enterprise Solution | SpotFire Decision Site for Functional Genomics ]

  

Definition of data mining software - Turnkey/Enterprise system

An Turnkey/Enterprise system defined as a computer system that is customized for a particular application and is usually designed for Enterprises, large institutions and big pharmaceutical companies. A microarray turnkey/enterprice Data Mining system can include everything like operating system, server software, database, client software, statistics software and even hardware customized for the whole Data Mining process.

Suggested data mining 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 - Turnkey/Enterprise system (in alphabetical order)

 
Product Company/ Institute Interface/Operating System Features Price Remarks
arraySCOUT LION bioscience AG Windows java client/various types of UNIX server Analyze expression data from various array format; allow integration of your own analysis method; share data and results on an enterprise-wide level; work with pathSCOUT to elucidate molecular pathway no pricing information is available -
BASE (BioArray Software Environment) Department of Oncology,
Lund University		 Linux server, MySQL, web client BASE is a comprehensive database server to manage the massive amounts of data generated by microarray analysis. It manages biomaterial information, raw data and images, and provides integrated and "plug-in"-able normalization, data viewing and analysis tools. The system also has array production LIMS features; supports MIAME and MAGE-ML Free, GNU GPL download;schema; textual description; specification; reference [PubMed]
Expressionist 3.1 GeneData UNIX, Linux, & Windows (server) and Windows, Unix, Linux, and Mac (client) normalization, cluster analysis, principal components analysis (PCA), support vector machine (SVM), K-means, SOM, MOPS and various distance metrics; proprietary SQL or Oracle based database; support both affy and spotted arrays; various quality control and visualization tools; supports MIAME
 depends on number of users Contact GeneData for a demo; brochures;product description;
GAAS (Gene Array Analyzer Software)
 Marco Masseroli & Pietro Cerveri, Bioengineering Department, Politecnico di Milano, Milano, Italy
MS-Windows 98/NT/2000/XP or Macintosh running the Virtual-PC software
 GAAS is an integrated software framework for management, analysis and visualization of large amounts of gene expression data across replicated experiments. It is designed for a multi-user environment, enabling each user to store its own parameter values used to perform the analyses, and define data visualization schema and format of the output data.
 Free
 Reference [PubMed]
Genedirector BioDiscovery Windows a microarray data management system that organize, archive, retrieve, analyze and query all microarray data throughout the entire workflow; built-in LIMS for project managment; Relation Database Design deployed on Oracle; Security control; integrate with Clonetracker, Imagene and Genesight for various stage of data analysis. no pricing information is available -
GeneSifter.Net VizX Labs Web client
 Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation from databases such as Unigene and LocusLink.
 no pricing information is available
 features;specifications;online demo; pdf fact sheet; tech reports; faq;
Genetraffic 2.6
 Iobion Informatics Linux server,
web client		 A turnkey system stores, analyzes and visualizes microarray expression data. Store raw data and images in a PostgreSQL relational database.  Supports the MIAME standards. Provides data management and data validation tools. Features include  normalization, hierarchical & K means clustering, PCA, multidimensional scaling and annotation storage.  no pricing information is available demo available (registration is required; limited to IE family browser only); screenshots;
Genowiz Ocimum Biosolutions Windows, Macintosh, Unix, Linux, Solaris Database module compliant with MIAME, Analysis Tracking, Data import and filtering, normalization, hierarchical, K-means/Forgy's clustering, SOMs, PCA, Data classification,  pathway analysis.
 no pricing information is available -
Rosetta Resolver Version 4.0 Rosetta Biosoftware JAVA/ UNIX with Oracle 8i relational database Error Models & Quality Statistics, clustering, K-means, K-median, SOMs, numerous visualization tools. Bayesian Class Prediction Algorithms, ANOVA, ROAST algorithm to search for genes with similar expression profiles Academic discounts available. -
SilicoCyte
 CytoGenomics Inc.
 Windows 2000 or XP professional
 Gene, probe & microarray annotations, Automatic gridding, Custom gene hierarchies, Data mining query builder, 3D scatter plots, Element Location Map Viewer, Clear-cut visual and numerical analysis, Comprehensive LIMS functionalities, Public & private database linkages. Full integration with SpotFire no pricing information is available brochure; demo upon registration; data sheet;
Silicon Genetics Enterprise Solution Silicon Genetics Windows 2000, Unix/ Linux server; windows, mac or unix/linux client combining GeNet database, GeneSpring datamining and Metamine as an enterprise solution for archiving, distribution and collaboration issues while maintaining all the independence and speed advantages of desktop computation no pricing information is available demo upon registration; pdf data sheet;
SpotFire Decision Site for Functional Genomics SpotFire Windows hierarchical, bi-directional hierarchical and K-means cluster analysis, PCA, profile search, coincidence testing, normalization, a number of interactive plots for visualization of data, access GATC databases no pricing information is available Information sheet

last updated: 23 Nov 2003
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