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首页> 外文期刊>Journal of Integrative Bioinformatics >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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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:/utrilyzer.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.
机译：有机体试图通过平衡地吸收环境中的营养来维持体内平衡。从原子角度看，这意味着例如将碳：氮：硫的比率保持在给定的限度内。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。硫的剥夺会导致富含硫的氨基酸（即甲硫酮和半胱氨酸）贫乏的同工型的上调。因此，富含硫的同工型被下调。我们开发了一种基于网络的软件，掺杂了Nutrilyzer，可从带注释的基因组序列中提取旁系蛋白质编码序列，并评估其原子组成。当获得营养限制和正常条件下的基因表达数据时，Nutrilyzer提供了一个基因列表，这些基因的表达差异显着，同时在原子组成中同时包含数量显着不同的有限营养。它的预期用途是在生态化学计量领域。可在http:/utrilyzer.hs-mittweida.de上找到Nutrilyzer。在这里，我们以缺氧时全基因组拟南芥基因表达分析为例，描述了工作流程和结果。发现分布在37个同源簇中的43个旁系同源物表达差异显着，而氧含量却显着不同。

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