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Best Microarray Data Analysis Software

Best Microarray Data Analysis Software

High quality image processing and appropriate data analysis are important steps of a microarray experiment. This BiologyWise article outlines some of the best microarray data analysis software available to extract statistically and biologically significant information from microarray experiments.
BiologyWise Staff
Did You Know?
A single microarray generates about 105 – 106 fragments of data.

Microarray experiments followed by accurate analysis of the enormous amount of data generated have developed to be a rich source of information with respect to several aspects of biology, including gene function, gene expression, pathway analysis, genomic comparisons, etc.

Given below are some of the best and most used comprehensive software that enable preprocessing, normalization, filtering, clustering, and finally, the biological interpretation and analysis of microarray data. In addition, specific software that provide tools for a particular type of analysis have also been described.

Bioconductor

Type: Free and open source
Maintained by: Fred Hutchinson Cancer Research Center
Operating System: Windows, Linux, Mac OS X
Functionality: Comprehensive

This open development project was initiated in 2001, and is based on the R programming language. It comprises R packages that provide statistical, graphical, and other computational tools for DNA microarray image processing and data analysis, sequence analysis, as well as SNP (Single Nucleotide Polymorphism) data analysis. Specific packages are available that cater to several commercial microarray platforms like Affymetrix.

In addition to this, it enables easy genome annotation through real-time association with GenBank, PubMed, and other databases containing genomic data and microarray data. These packages, being open-source in nature, can be modified in order to cater to particular experimental requirements. However, the use of Bioconductor packages require the user to have an experience with the R environment, and some may find the interface a bit difficult to follow.

TM4 Microarray Software Suite

Type: Free and open source
Maintained by: Institute for Genomic Research and other contributors
Operating System: Windows, Linux, Mac OS X
Functionality: Comprehensive

The TM4 Microarray Software Suite provides the following applications that have been developed in Java and C/C++.
  1. MADAM (Microarray Data Manager) is developed to manage and store microarray data as well as the associated information, like experimental design, parameters, protocols, etc. This data is stored in a MySQL database in accordance with the MIAME (Minimal Information About a Microarray Experiment) standards.
  2. MIDAS (Microarray Data Analysis System) is developed for normalizing and filtering the data obtained. The resultant output is stored in .tav format in the MADAM associated database.
  3. Spotfinder is designed for rapid image processing and quantification of signals at each spot to quantify gene expression.
  4. MeV (MultiExperiment Viewer) enables the analysis of the normalized and filtered microarray data. It provides tools for clustering and classification, graphical visualization, statistical analysis, as well as annotation.
  5. AMP (Automated Microarray Pipeline) is a web-based application where microarray data in the form of Affymetrix CEL files can be submitted for further analysis. The workflow or pipeline can be specified for normalization and statistical analysis followed by gene classification and annotation. AMP is comparatively user-friendly, and the results are displayed in a web-based format which can be easily stored and used for further analysis.
In addition to these applications, two supportive utilities, like the ExpressConverter and SlideMap are also available. The ExpressConverter enables quick conversions of files from one format to the other, whereas the SlideMap is a Perl module that helps create a map of the experimental microarray slide.

GenePattern

Type: Free and open source, as well as in the form of a public web server
Maintained by: Broad Institute
Operating System: Windows, Linux, Ubuntu, SuSE, CentOS, Mac OS 10.7 and later
Functionality: Comprehensive

Developed using the R programing language, this is a highly user-friendly system and comprises several analysis modules that can be easily arranged and interconnected to form a customized pipeline. Microarray data can be normalized, preprocessed, and analyzed for gene expression patterns, predicting the class of desired genes, clustering and discovering the gene class, as well as pathway analysis.

These functionalities can be availed locally by installing the software, or by registering on the public web server available on the website for Broad Institute. Once registered, users can login and create pipelines, analyze their data, and save their analyses and results. This powerful workflow management system is highly biologist-friendly and merely requires the knowledge of file formats. Programming skills or expertise with the R environment is not required.

GenMAPP

Type: Free and open source
Maintained by: GenMAPP.org
Operating System: Windows
Functionality: Specific

Developed using Visual Basic 6.0, GenMAPP or the Gene Map Annotator and Pathway Profiler is specifically designed for the analysis of genomic microarray data for understanding and identifying biological pathways, like anabolic and catabolic pathways as well as signaling pathways.

It contains gene databases for selected model organisms, including E.coli, humans, mouse, zebrafish, etc. The gene expression data obtained from custom as well as commercial microarrays can be analyzed, and the desired genes can be visualized in the form of a pathway by using a color-coded format as per the criteria indicated by the user. It provides tools to construct and modify pathways using earlier information about gene annotations.

In addition, it facilitates free and easy exchange of pathway information amongst different investigators, thus, facilitating collaborative studies. The biological pathways are stored in a format called MAPP, and these MAPPs can be easily shared and even converted to HTML format.

ImaGene

Type: Commercial
Provided by: BioDiscovery
Operating System: Windows, Mac, and Linux
Functionality: Comprehensive

This is a Java-based commercial software for analyzing data from almost any platform and type of microarray. It even provides ready-to-use templates for standard microarray platforms, like Agilent 244K, 4x44K, 44K arrays, etc.

It provides applications for high-quality image processing, normalization, preprocessing, and subsequent data analysis for DNA, microRNA, as well as protein microarrays. It also enables array comparative genomic hybridization (aCGH) analysis. A distinguishing feature is the batch processing of data from multiple microarray images, which increases the convenience quotient and reduces the time invested in processing and analyzing all the samples.

Others

✦ Integromics Biomarker Discovery
✦ Spotfire DecisionSite for Functional Genomics
✦ GeneSpring
✦ Babelomics 4.3
✦ BRB-ArrayTools
✦ INCLUSive
✦ GenePublisher 1.03
✦ ChipInfo
✦ GeneSifter
✦ ExpressYourself

Analyzing microarray data depends on the type of microarray as well as the design of the study. In addition to convenience, the choice of microarray data analysis software and the statistical analysis tools should be made after careful consideration of the experimental conditions and precise objective.