Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.
复制标题
DOI：
10.1371/journal.pcbi.1010174
复制
发表时间：
2022-06
影响因子：
4.3
通讯作者：
中科院分区：
文献类型：
--
作者：
公共领域中越来越多的蛋白质组学数据使得除其他应用外，数据集的组合分析能够创建覆盖不同生物体和不同生物条件的比较蛋白质表达图谱。在这里，我们重新分析了来自小鼠和大鼠组织的公共蛋白质组学数据集（分别为14和9个数据集），以评估基线蛋白质丰度。总体而言，汇总数据集包含23个单独的数据集，包括来自14个器官的34个不同组织的总计211个样本，分别包括9个小鼠和3个大鼠品系。在所有情况下，我们研究了典型蛋白质在不同器官之间的分布。每个数据集的典型蛋白质数量在小鼠中为273（肌腱）和9，715（肝脏），在大鼠中为101（肌腱）和6，130（肾脏）。然后，我们研究了两个物种在不同数据集和器官中的蛋白质丰度如何进行比较。作为一个关键点，我们进行了小鼠，大鼠和人体组织之间的蛋白质表达的比较分析。我们观察到在脑、肾、心脏和肝脏样品中所有三个物种之间的直系同源物之间蛋白质表达的高水平相关性，而同一物种内器官之间蛋白质表达的相关性通常略低。蛋白质表达结果已被整合到资源表达图谱中以广泛传播。我们重新分析了PRIDE数据库中存储的23个基于质谱的基线公共蛋白质组学数据集。总体而言，汇总数据集包含211个样本，来自14个器官的34个不同组织，分别包括9个小鼠和3个大鼠品系。我们分析了这两个物种中蛋白质表达在器官中的分布。我们还研究了两个物种在不同数据集和器官中的蛋白质丰度如何进行比较。然后，我们进行了基因本体和途径富集分析，以确定跨器官的富集生物过程和途径。我们还对小鼠、大鼠和人体组织中的基线蛋白表达进行了比较分析，观察到所有三个物种的脑、肾、心脏和肝脏样品中直系同源物之间的高水平表达相关性。为了传播这些发现，我们将蛋白质表达结果整合到资源Expression Atlas中。
The increasingly large amount of proteomics data in the public domain enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination. We have reanalysed 23 baseline mass spectrometry-based public proteomics datasets stored in the PRIDE database. Overall, the aggregated dataset contained 211 samples, coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We analysed the distribution of protein expression across organs in both species. We also studied how protein abundances compared across different datasets and organs for both species. Then we performed gene ontology and pathway enrichment analyses to identify enriched biological processes and pathways across organs. We also carried out a comparative analysis of baseline protein expression across mouse, rat and human tissues, observing a high level of expression correlation among orthologs in all three species, in brain, kidney, heart and liver samples. To disseminate these findings, we have integrated the protein expression results into the resource Expression Atlas.
影响因子：
4.4
作者：
Prasad A;Kumar SS;Dessimoz C;Bleuler S;Laule O;Hruz T;Gruissem W;Zimmermann P
通讯作者：
Zimmermann P