Journal of Integrative Bioinformatics, 11(1):235, 2014 http://journal.imbio.de/ Integrated visualization of a multi-omics study of starvation in mouse intestine Martijn P. van Iersel 1,2,3 , Milka Sokolovi´ c 4,5 , Kaatje Lenaerts 6 , Martina Kutmon 1,2 , Freek G. Bouwman 7 , Wouter H. Lamers 8 , Edwin C.M. Mariman 7 and Chris T. Evelo 1,2,* 1 Department of Bioinformatics BiGCaT, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, The Netherlands 2 Netherlands Consortium for Systems Biology (NCSB), The Netherlands 3 Current address: General Bioinformatics, Reading, UK 4 Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands 5 European Food Information Council, Brussels, Belgium 6 Department of Surgery, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, The Netherlands 7 Department of Human Biology, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, The Netherlands 8 Tytgat Institute for Liver and Intestinal Research (formerly AMC Liver Center), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands Summary Our understanding of complex biological processes can be enhanced by combining dif- ferent kinds of high-throughput experimental data, but the use of incompatible identifiers makes data integration a challenge. We aimed to improve methods for integrating and vi- sualizing different types of omics data. To validate these methods, we applied them to two previous studies on starvation in mice, one using proteomics and the other using transcrip- tomics technology. We extended the PathVisio software with new plugins to link proteins, transcripts and path- ways. A low overall correlation between proteome and transcriptome data was detected (Spearman rank correlation: 0.21). At the level of individual genes, correlation was highly variable. Many mRNA/protein pairs, such as fructose biphosphate aldolase B and ATP Synthase, show good correlation. For other pairs, such as ferritin and elongation factor 2, an interesting effect is observed, where mRNA and protein levels change in opposite * To whom correspondence should be addressed. Email: chris.evelo@maastrichtuniversity.nl doi:10.2390/biecoll-jib-2014-235 1 Copyright 2014 The Author(s). Published by Journal of Integrative Bioinformatics. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/).