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TM4 News

1/18/08 - MeV v4.1 is now available for download
See the release notes for details.

1/29/07 - ExpressConverter v1.9 is now available for download
See the release notes for details.

07/06/06 - MeV 4.0 leaves beta testing
MeV v4.0 has come out of beta testing. A few bugs were found and fixed, including a bug that prevented state-saving on the Mac and Linux platforms. See the release notes and the MeV page for more details.

05/15/06 - MeV 4.0beta Released
MeV v4.0b is now available for download. New features include Robust Analysis of MicroArrays (RAMA), Comparative Genomic Hybridization Viewer & Analyzer, Linear Expression Mapping (LEM), Tree-EASE (TEASE), Bayesian Robust Inference for Differential Gene Expression (BRIDGE), Uncorrelated Shrunken Centroids (USC) and many smaller improvements and bux-fixes. See the release notes and the MeV page for more details.

02/25/05 - MeSHer Released
MeSHer is a Java tool for biological literature mining. The program performs a statistical analyis of MeSH (Medical Subject Headings) terms to find over-represented biological themes in a given sample of genes as compared with a larger population of genes.
Download the source code for the stand-alone application here.
Try MeSHer online

What is TM4?

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 allow for assays of tremendous complexity and scope. Scientist seeking to harness the potential of this technique are often challenged by the prodigious 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 TIGR's Software Download Site. 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). Three of the TM4 applications, MADAM, MIDAS, and MeV, were developed in Java; TIGR Spotfinder was written in C/C++. 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 new analysis methods and utilities that will further enhance the capabilities of this software system.

TM4 is free, open-source software released under the Artistic license. This license is OSI certified.

Getting TM4

The individual components of the TM4 package are downloadable from this site. Simply select the program you wish to download from the listing on the right of this page. TM4 CDs, (picture right) are available at the various courses taught by our group. You can see a list of these courses here.

TM4 requires Java v1.4.1 or higher. Spotfinder, MIDAS and MeV require Windows 2000/XP, MacOSX or Linux. MADAM currently only runs on Windows 2000/XP. Hardware requirements for all of these packages depend on the size of data sets used.

Referencing TM4

The TM4 system is fully described in:
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374-8.

Latest Version: v4.0 v4.0
MADAM (MicroArray DAta Manager) is a java-based application designed to load and retrieve microarray data to and from a database (also supplied with the software).

Latest Version: v3.1.1
Linux / Mac OSX / Win
TIGR Spotfinder is a software tool designed for Microarray image processing using the TIFF image files generated by most microarray scanners.

Latest Version: v2.19
TIGR Microarray Data Analysis System (MIDAS) is a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline.

Latest Version: v4.1
Older Version: v4.0
MultiExperiment Viewer (MeV) is a Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes.

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