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

References in zbMATH (referenced in 11 articles )

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  1. Mestizo Gutiérrez, Sonia L.; Herrera Rivero, Marisol; Cruz Ramírez, Nicandro; Hernández, Elena; Aranda-Abreu, Gonzalo E.: Decision trees for the analysis of genes involved in Alzheimer’s disease pathology (2014)
  2. Lehrmann, Andreas; Huber, Michael; Polatkan, Aydin C.; Pritzkau, Albert; Nieselt, Kay: Visualizing dimensionality reduction of systems biology data (2013) ioport
  3. Panigrahi, Priya P.; Singh, Tiratha Raj: Computational studies on Alzheimer’s disease associated pathways and regulatory patterns using microarray gene expression and network data: revealed association with aging and other diseases (2013)
  4. Guzzi, Pietro H.; Di Martino, Maria Teresa; Tradigo, Giuseppe; Veltri, Pierangelo; Tassone, Pierfrancesco; Tagliaferri, Pierosandro; Cannataro, Mario: Automatic summarisation and annotation of microarray data (2011) ioport
  5. Guzzi, Pietro Hiram; Cannataro, Mario: Mu-CS: an extension of the TM4 platform to manage affymetrix binary data (2010) ioport
  6. Mitra, Ramkrishna; Bandyopadhyay, Sanghamitra; Maulik, Ujjwal; Zhang, Michael Q.: Sfssclass: an integrated approach for mirna based tumor classification (2010) ioport
  7. Tang, DongMing; Zhu, QingXin; Yang, Fan: A Poisson-based adaptive affinity propagation clustering for SAGE data (2010)
  8. Schwager, Christian; Abdollahi, Amir; Wirkner, Ute; Huber, Peter: Tablebutler - A tool for combining, handling and processing of huge data tables (2009) ioport
  9. Hulshizer, Randall; Blalock, Eric M.: (Post hoc )pattern matching: Assigning significance to statistically defined expression patterns in single channel microarray data (2007) ioport
  10. Marco, Antonio; Marin, Ignacio: A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification (2007) ioport
  11. Marzolf, Bruz; Deutsch, Eric W.; Moss, Patrick; Campbell, David; Johnson, Michael H.; Galitski, Timothy: SBEAMS-microarray: Database software supporting genomic expression analyses for systems biology (2006) ioport