Matrix2png: a utility for visualizing matrix data - PubMed (original) (raw)

Matrix2png: a utility for visualizing matrix data

Paul Pavlidis et al. Bioinformatics. 2003.

Abstract

We describe a simple software tool, 'matrix2png', for creating color images of matrix data. Originally designed with the display of microarray data sets in mind, it is a general tool that can be used to make simple visualizations of matrices for use in figures, web pages, slide presentations and the like. It can also be used to generate images 'on the fly' in web applications. Both continuous-valued and discrete-valued (categorical) data sets can be displayed. Many options are available to the user, including the colors used, the display of row and column labels, and scale bars. In this note we describe some of matrix2png's features and describe some places it has been useful in the authors' work.

Availability: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request.

PubMed Disclaimer

Similar articles

• Genomic data visualization on the Web.
  Wu W, Noble WS. Wu W, et al. Bioinformatics. 2004 Jul 22;20(11):1804-5. doi: 10.1093/bioinformatics/bth154. Epub 2004 Feb 26. Bioinformatics. 2004. PMID: 14988106
• Applications of Tree-Maps to hierarchical biological data.
  McConnell P, Johnson K, Lin S. McConnell P, et al. Bioinformatics. 2002 Sep;18(9):1278-9. doi: 10.1093/bioinformatics/18.9.1278. Bioinformatics. 2002. PMID: 12217926
• IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform.
  Schultze JL, Eggle D. Schultze JL, et al. Bioinformatics. 2007 Jun 1;23(11):1431-3. doi: 10.1093/bioinformatics/btm101. Epub 2007 Mar 23. Bioinformatics. 2007. PMID: 17384020
• An overview of Spotfire for gene-expression studies.
  Kaushal D, Naeve CW. Kaushal D, et al. Curr Protoc Bioinformatics. 2004 Sep;Chapter 7:Unit 7.7. doi: 10.1002/0471250953.bi0707s6. Curr Protoc Bioinformatics. 2004. PMID: 18428733 Review.
• A survey of metabolic databases emphasizing the MetaCyc family.
  Karp PD, Caspi R. Karp PD, et al. Arch Toxicol. 2011 Sep;85(9):1015-33. doi: 10.1007/s00204-011-0705-2. Epub 2011 Apr 27. Arch Toxicol. 2011. PMID: 21523460 Free PMC article. Review.

Cited by

• Enhanced cardiac Akt/protein kinase B signaling contributes to pathological cardiac hypertrophy in part by impairing mitochondrial function via transcriptional repression of mitochondrion-targeted nuclear genes.
  Wende AR, O'Neill BT, Bugger H, Riehle C, Tuinei J, Buchanan J, Tsushima K, Wang L, Caro P, Guo A, Sloan C, Kim BJ, Wang X, Pereira RO, McCrory MA, Nye BG, Benavides GA, Darley-Usmar VM, Shioi T, Weimer BC, Abel ED. Wende AR, et al. Mol Cell Biol. 2015 Mar;35(5):831-46. doi: 10.1128/MCB.01109-14. Epub 2014 Dec 22. Mol Cell Biol. 2015. PMID: 25535334 Free PMC article.
• Dedifferentiation of neurons and astrocytes by oncogenes can induce gliomas in mice.
  Friedmann-Morvinski D, Bushong EA, Ke E, Soda Y, Marumoto T, Singer O, Ellisman MH, Verma IM. Friedmann-Morvinski D, et al. Science. 2012 Nov 23;338(6110):1080-4. doi: 10.1126/science.1226929. Epub 2012 Oct 18. Science. 2012. PMID: 23087000 Free PMC article.
• The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival.
  Chen F, Zhang Y, Shen L, Creighton CJ. Chen F, et al. Nat Commun. 2024 Aug 8;15(1):6775. doi: 10.1038/s41467-024-51276-y. Nat Commun. 2024. PMID: 39117669 Free PMC article.
• Integrative bioinformatics analysis of genomic and proteomic approaches to understand the transcriptional regulatory program in coronary artery disease pathways.
  Vangala RK, Ravindran V, Ghatge M, Shanker J, Arvind P, Bindu H, Shekar M, Rao VS. Vangala RK, et al. PLoS One. 2013;8(2):e57193. doi: 10.1371/journal.pone.0057193. Epub 2013 Feb 28. PLoS One. 2013. PMID: 23468932 Free PMC article.
• Potential of six-transmembrane epithelial antigen of the prostate 4 as a prognostic marker for colorectal cancer.
  Fang ZX, Li CL, Chen WJ, Wu HT, Liu J. Fang ZX, et al. World J Gastrointest Oncol. 2022 Sep 15;14(9):1675-1688. doi: 10.4251/wjgo.v14.i9.1675. World J Gastrointest Oncol. 2022. PMID: 36187390 Free PMC article.

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.
  • Silverchair Information Systems

• Other Literature Sources

  • The Lens - Patent Citations Database