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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 11, Issue 1

Issues

Integrated visualization of a multi-omics study of starvation in mouse intestine

Martijn P. van Iersel
  • Department of Bioinformatics BiGCaT, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, United Kingdom of Great Britain and Northern Ireland
  • Netherlands Consortium for Systems Biology (NCSB), Amsterdam, United Kingdom of Great Britain and Northern Ireland
  • General Bioinformatics, Reading, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Milka Sokolović
  • Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam Belgium
  • European Food Information Council, Brussels, Belgium
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Kaatje Lenaerts
  • Department of Surgery, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Martina Kutmon
  • Department of Bioinformatics BiGCaT, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht Netherlands
  • Netherlands Consortium for Systems Biology (NCSB), Amsterdam, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Freek G. Bouwman
  • Department of Human Biology, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Wouter H. Lamers
  • Department of Bioinformatics BiGCaT, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, United Kingdom of Great Britain and Northern Ireland
  • Tytgat Institute for Liver and Intestinal Research (formerly AMC Liver Center), Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Edwin C.M. Mariman
  • Department of Human Biology, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Chris T. Evelo
  • Corresponding author
  • Department of Bioinformatics BiGCaT, NUTRIM School for Nutrition, Toxicology, and Metabolism, Maastricht University, Maastricht Netherlands
  • Netherlands Consortium for Systems Biology (NCSB), Amsterdam, Netherlands
  • Email
  • Other articles by this author:
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2014-235

Summary

Our understanding of complex biological processes can be enhanced by combining different 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 visualizing 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 transcriptomics technology. We extended the PathVisio software with new plugins to link proteins, transcripts and pathways. 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 directions, suggesting they are not primarily regulated at the transcriptional level. We used pathway diagrams to visualize the integrated datasets and found it encouraging that transcriptomics and proteomics data supported each other at the pathway level. Visualization of the integrated dataset on pathways led to new observations on gene-regulation in the response of the gut to starvation. Our methods are generic and can be applied to any multi-omics study. The PathVisio software can be obtained at http://www.pathvisio.org. Supplemental data are available at http://www.bigcat.unimaas.nl/data/jib-supplemental/, including instructions on reproducing the pathway visualizations of this manuscript.

About the article

Published Online: 2016-10-18

Published in Print: 2014-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 11, Issue 1, Pages 1–16, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2014-235.

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© 2014 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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