TM4: a free, open-source system for microarray data management and analysis.

By A. Saeed, V. Sharov, J. White, J. Li, W. Liang, N. Bhagabati, J. Braisted, M. Kłapa, T. Currier, M. Thiagarajan and 11 more. BioTechniques, 2003

4,918 citations recorded by the source corpus.

White1, J. Li1, W. Liang1, N. Bhagabati1, J. Braisted1, M. Klapa1, T. Currier1, M. Thiagarajan1, A. Sturn1, M. Snuffin2, A. Rezantsev2, D. Popov2, A. Ryltsov2, E. Kostukovich2, I. Borisovsky2, Z. Liu3, A. Vinsavich3, V. Trush3, and J. Quackenbush1,4 1The Institute for Genomic Research, Rockville, MD, 2DataNaut, Bethesda, MD, 3Syntek Systems, Bethesda, MD, and 4Department of Biochemistry, George Washington University, Washington, D.C., USA

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/04eaa03dc670afa88c9f3c83fc8da08ef4d31cdd

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Citations in the corpus

STEM: a tool for the analysis of short time series gene expression data (2006, methodology): “These include Cluster [7], EXPANDER [18], the MultiExperiment Viewer [19], and the High-Through-put Miner [20] among many others.”
An interferon-related gene signature for DNA damage resistance is a predictive marker for chemotherapy and radiation for breast cancer (2008, methodology): “0 (9) for each of the microarray data sets with a k value of 2 and requiring 90% consensus for each of the two clusters after 500 runs.”
Inaugural Article: The protein expression landscape of the Arabidopsis root (2012, positive): “Heat maps of the resulting spatial clusters of the root cellular proteome were generated using MultiExperimentViewer software (version4) (67, 68).”
Using graph theory to analyze biological networks (2011, methodology): “Known platforms that already share the tree-based algorithms described above are the Hierarchical Clustering Explorer (HCE) [122,123], MEGA [124-127] or TM4 [128].”
Expression profiling identifies microRNA signature in pancreatic cancer (2006, methodology): “To compare the expression patterns of differentially expressed genes, the filtered data were analyzed using hierarchical clustering of samples and hierarchical clustering of genes based on average linkage and Euclidian distance.(30,31)”
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes (2013, methodology): “Data were ordered and grouped using the distance matrix computation and hierarchical clustering analysis calculated by MultiExperimentViewer [82].”