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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

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 9, Issue 2

Issues

Nutrilyzer: A Tool for Deciphering Atomic Stoichiometry of Differentially Expressed Paralogous Proteins

Katrin Lotz / Falk Schreiber
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Gatersleben, Germany Germany
  • Martin Luther University Halle-Wittenberg, Institute of Computer Science, Von-Seckendorff-Platz 1, 06120 Halle, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Röbbe Wünschiers
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2012-196

Summary

Organisms try to maintain homeostasis by balanced uptake of nutrients from their environment. From an atomic perspective this means that, for example, carbon:nitrogen:sulfur ratios are kept within given limits. Upon limitation of, for example, sulfur, its acquisition is triggered. For yeast it was shown that transporters and enzymes involved in sulfur up- take are encoded as paralogous genes that express different isoforms. Sulfur deprivation leads to up-regulation of isoforms that are poor in sulfur-containing amino acids, that is, methinone and cysteine. Accordingly, sulfur-rich isoforms are down-regulated.

We developed a web-based software, doped Nutrilyzer, that extracts paralogous protein coding sequences from an annotated genome sequence and evaluates their atomic compo- sition. When fed with gene-expression data for nutrient limited and normal conditions, Nutrilyzer provides a list of genes that are significantly differently expressed and simul- taneously contain significantly different amounts of the limited nutrient in their atomic composition. Its intended use is in the field of ecological stoichiometry. Nutrilyzer is available at http://nutrilyzer.hs-mittweida.de.

Here we describe the work flow and results with an example from a whole-genome Ara- bidopsis thaliana gene-expression analysis upon oxygen deprivation. 43 paralogs distributed over 37 homology clusters were found to be significantly differently expressed while containing significantly different amounts of oxygen.

About the article

Published Online: 2016-10-18

Published in Print: 2012-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 9, Issue 2, Pages 46–52, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2012-196.

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© 2012 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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