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首页> 外文会议>International symposium on integrative bioinformatics, 8th annual meeting >Nutrilyzer: A Tool for Deciphering Atomic Stoichiometry of Differentially Expressed Paralogous Proteins
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Nutrilyzer: A Tool for Deciphering Atomic Stoichiometry of Differentially Expressed Paralogous Proteins

机译：Nutrilyzer：破译差异表达旁系蛋白质的原子化学计量的工具

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摘要

Organisms try to maintain homeostasis by balanced uptake of nutrients from their envi-ronment 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 upregulation of isoforms (hat are poor in sulfurcontaining amino acids, that is, methinone and cysteine. Accordingly, sulfur-rich isoforms are downregulated. 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 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: /utrilyzer .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 dis-tributed over 37 homology clusters were found to be significantly differently expressed while containing significantly different amounts of oxygen.
机译：有机体试图通过平衡从环境中吸收养分来维持体内平衡。从原子的角度来看，这意味着，例如，碳：氮：硫的比率应保持在给定的范围内。在例如限制硫的情况下，触发其获取。对于酵母，已表明参与硫吸收的转运蛋白和酶被编码为表达不同同工型的旁系基因。硫的剥夺导致同工型的上调（帽子中含硫氨基酸，即蛋氨酸和半胱氨酸含量低）。因此，富硫同工型被下调。我们开发了基于网络的软件，掺杂的Nutrilyzer，可从当获得营养有限和正常条件下的基因表达数据时，Nutrilyzer会提供一系列基因的表达，这些基因的表达差异显着，同时原子中包含的营养限含量也明显不同Nutrilyzer可在http://nutrilyzer.hs-mittweida.de上获得，此处我们以全基因组Ara-bidopsis thaliana基因为例来描述工作流程和结果。氧缺乏的表达分析发现分布在37个同源簇中的43个旁系同源物氧含量显着不同，但表达差异很大。

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  • 会议地点 Hangzhou(CN)
  • 作者

    Katrin Lotz; Falk Schreiber; Robbe Wiinschiers;

  • 作者单位

    SunGene GmbH, Corrensstr. 3, D-06466 Gatersleben, Germany;

    Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben,Corrensstr. 3, D-06466 Gatersleben, Germany Martin Luther University Halle-Wittenberg, Institute of Computer Science,Von-Seckendorff-Platz 1, 06120 Halle, Germany;

    University of Applied Sciences Mittweida, Technikumplatz 17,09648 Mittweida, Germany;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物信息论;
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