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

作者：A Saeed, Vasily Sharov, Joseph Robert White, Jiatong Li, Wei Ping Liang, NIRMAL K. BHAGABATI, John C. Braisted, Maria I. Klapa, Tracey Currier, Mathangi Thiagarajan, Alexander Sturn, M. Snuffin, A. Rezantsev, Д. А. Попов, A. Ryltsov, E. Kostukovich, I. Borisovsky, Z. Liu, A. Vinsavich, V. Trush, John Quackenbush · 发表于：BioTechniques · 年份：2003 · DOI：10.2144/03342mt01 · 被引用次数：4991 · 研究领域：Gene expression and cancer classification、Bioinformatics and Genomic Networks、Evolutionary Algorithms and Applications

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 ® , Un...