TM4: A Free, Open-Source System for Microarray Data Management and Analysis

Microarrays have emerged as the premier tool for studying gene expression on a genomic scale. Advances in the precision of array printers and scanners as well as improved laboratory protocols (11) allow for assays of tremendous complexity and scope. Scientists seeking to harness the potential of this technique are often challenged by the large quantities of data produced. Well-designed, user-friendly software is the key to tracking, integrating, qualifying, and ultimately deriving scientific insight from the experimental results. In support of our ongoing work in microarray analysis of gene expression, we developed a suite of software that allow users in the laboratory to capture, manage, and analyze effectively data from DNA microarray experiments. The TM4 suite of tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer (MeV), as well as a Minimal Information About a Microarray Experiment (MIAME)-compliant MySQL database, all of which are freely available to the scientific research community at http://www.tigr.org/software. Although these software tools were developed for spotted two-color arrays, many of the components can be easily adapted to work with single-color formats such as filter arrays and GeneChips (Affymetrix, Santa Clara, CA, USA). Three of the TM4 applications, MADAM, MIDAS, and MeV, were developed in Java and have been tested on Microsoft Windows, Linux , Unix , and MacOS X platforms; TIGR Spotfinder was written in C/C++ and runs only on Windows systems. The TM4 software system represents a comprehensive, extensible, open-source, and freely available collection of tools that we believe will be of use to a wide range of laboratories conducting microarray experiments. We further hope that by providing source code along with the executable software, we can encourage others to develop new analysis methods and utilities that will further enhance the capabilities of this software system.