小鼠胚胎 CoCoPUTs:具有多个品系、组织和阶段的新型小鼠转录组加权使用网站。

IF 2.9 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS
Sarah E Fumagalli, Sean Smith, Tigran Ghazanchyan, Douglas Meyer, Rahul Paul, Collin Campbell, Luis Santana-Quintero, Anton Golikov, Juan Ibla, Haim Bar, Anton A Komar, Ryan C Hunt, Brian Lin, Michael DiCuccio, Chava Kimchi-Sarfaty
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引用次数: 0

摘要

小鼠(Mus musculus)模型在发育生物学研究中被大量用于了解哺乳动物的胚胎发育,因为小鼠与人类有许多共同的遗传、生理和发育特征。对整合时间(阶段特异性)和转录(组织特异性)数据的新探索扩大了我们对小鼠胚胎组织特异性基因功能的了解。为了更好地了解细胞状态特异性转录组中的同义突变对组织的密码子和密码子对使用情况的重大影响,我们建立了一个新的资源--小鼠胚胎密码子和密码子对使用表(Mouse Embryo CoCoPUTs)。该网页不仅提供密码子和密码子对的使用情况,还提供 GC、二核苷酸和连接二核苷酸的使用情况,涵盖 4 个品系、15 个小鼠胚胎组织组、18 个 Theiler 阶段和 26 个胚胎日。在这里,我们利用小鼠胚胎 CoCoPUTs 并使用热图来描述每个品系和胚胎时间点的用量随时间的变化以及与人类用量的比较,突出了独特的差异和相似性。在小鼠和人类中枢神经系统数据之间发现的用法相似性突出了利用小鼠模型的项目转化。用于该分析的数据可直接从小鼠胚胎 CoCoPUTs 中获取。这一尖端资源在解读使用模式与胚胎发育之间复杂的相互作用方面发挥着至关重要的作用,为了解不同组织、品系和阶段的变异提供了宝贵的信息。它的应用涉及多个领域,在生物治疗开发方面具有显著优势,因为优化密码子的使用可以提高蛋白质的表达;人们可以在一次查询中比较品系、组织和小鼠胚胎阶段。此外,小鼠胚胎 CoCoPUTs 在组织特异性基因工程领域具有巨大的潜力,它为针对特定组织的基因表达进行有针对性的干预提供了见解。此外,该资源还能加深我们对使用偏差和组织特异性基因功能之间细微联系的理解,有助于开发更准确的遗传疾病预测模型。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.

Mouse (Mus musculus) models have been heavily utilized in developmental biology research to understand mammalian embryonic development, as mice share many genetic, physiological, and developmental characteristics with humans. New explorations into the integration of temporal (stage-specific) and transcriptional (tissue-specific) data have expanded our knowledge of mouse embryo tissue-specific gene functions. To better understand the substantial impact of synonymous mutational variations in the cell-state-specific transcriptome on a tissue's codon and codon pair usage landscape, we have established a novel resource-Mouse Embryo Codon and Codon Pair Usage Tables (Mouse Embryo CoCoPUTs). This webpage not only offers codon and codon pair usage, but also GC, dinucleotide, and junction dinucleotide usage, encompassing four strains, 15 murine embryonic tissue groups, 18 Theiler stages, and 26 embryonic days. Here, we leverage Mouse Embryo CoCoPUTs and employ the use of heatmaps to depict usage changes over time and a comparison to human usage for each strain and embryonic time point, highlighting unique differences and similarities. The usage similarities found between mouse and human central nervous system data highlight the translation for projects leveraging mouse models. Data for this analysis can be directly retrieved from Mouse Embryo CoCoPUTs. This cutting-edge resource plays a crucial role in deciphering the complex interplay between usage patterns and embryonic development, offering valuable insights into variation across diverse tissues, strains, and stages. Its applications extend across multiple domains, with notable advantages for biotherapeutic development, where optimizing codon usage can enhance protein expression; one can compare strains, tissues, and mouse embryonic stages in one query. Additionally, Mouse Embryo CoCoPUTs holds great potential in the field of tissue-specific genetic engineering, providing insights for tailoring gene expression to specific tissues for targeted interventions. Furthermore, this resource may enhance our understanding of the nuanced connections between usage biases and tissue-specific gene function, contributing to the development of more accurate predictive models for genetic disorders.

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来源期刊
BMC Bioinformatics
BMC Bioinformatics 生物-生化研究方法
CiteScore
5.70
自引率
3.30%
发文量
506
审稿时长
4.3 months
期刊介绍: BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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