Universität Bielefeld Electronic Collections animiertes Foto Universität Bielefeld

Access to the Document



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

Lotz, Katrin ; Schreiber, Falk ; Wunschiers, Robbe

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


Download file

Abstract:
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 uptake 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 composition. When fed with gene-expression data for nutrient limited and normal conditions, Nutrilyzer provides a list of genes that are significantly differently expressed and simultaneously 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 Arabidopsis 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.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Lotz, Katrin ; Schreiber, Falk ; Wunschiers, Robbe  (2012)  Nutrilyzer: A Tool for Deciphering Atomic Stoichiometry of Differentially Expressed Paralogous Proteins. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 9(2): Special Issue: 7th International Symposium on Integrative Bioinformatics, Hangzhou, China, 2012

Online-Journal: http://journal.imbio.de/article.php?aid=196
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2012/5223



 Questions or comments: publikationsdienste.ub@uni-bielefeld.de
 Latest update: 15 Feb 2011
 Legal Notice
OPUS-Logo     OAI compliant      BU Logo
OAI-Logo