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Paintomics: a Web Based Tool for the Joint Visualization of Transcriptomics and Metabolomics Data

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2010 Nov 25
PMID 21098431
Citations 70
Authors
Fernando Garcia-Alcalde
Federico Garcia-Lopez
Joaquin Dopazo
Ana Conesa
Affiliations
Soon will be listed here.
Abstract

Motivation: The development of the omics technologies such as transcriptomics, proteomics and metabolomics has made possible the realization of systems biology studies where biological systems are interrogated at different levels of biochemical activity (gene expression, protein activity and/or metabolite concentration). An effective approach to the analysis of these complex datasets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways.

Results: We have developed the Paintomics web server as an easy-to-use bioinformatics resource that facilitates the integrated visual analysis of experiments where transcriptomics and metabolomics data have been measured on different conditions for the same samples. Basically, Paintomics takes complete transcriptomics and metabolomics datasets, together with lists of significant gene or metabolite changes, and paints this information on KEGG pathway maps.

Availability: Paintomics is freely available at http://www.paintomics.org.

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References
1.
Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View
2.
Neuweger H, Persicke M, Albaum S, Bekel T, Dondrup M, Huser A . Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Syst Biol. 2009; 3:82. PMC: 2744654. DOI: 10.1186/1752-0509-3-82. View
3.
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T . KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol. 2005; 138(3):1289-300. PMC: 1176402. DOI: 10.1104/pp.105.060525. View
4.
Suhre K, Schmitt-Kopplin P . MassTRIX: mass translator into pathways. Nucleic Acids Res. 2008; 36(Web Server issue):W481-4. PMC: 2447776. DOI: 10.1093/nar/gkn194. View
5.
Kolbe A, Oliver S, Fernie A, Stitt M, van Dongen J, Geigenberger P . Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Physiol. 2006; 141(2):412-22. PMC: 1475465. DOI: 10.1104/pp.106.081208. View