Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.
J Proteome Res. 2011 Apr 1;10(4):1893-903. doi: 10.1021/pr101132h. Epub 2011 Feb 22.
Tissue-specific gene expression can result in the presence or absence of certain protein interactions and complexes, leading to profound functional differences of biological processes between the tissues. In this study, we integrate human gene expression data based on RNA-sequencing with protein interactions, domains and complexes to analyze the functional implications of their tissue specificity. This reveals that tissue specificity is characterized by much fewer proteins, domains, interactions, and complexes than previously thought. In contrast to previous microarray studies, our analysis based on RNA-sequencing suggests that tissue-specific protein interactions are less common and mainly involved with transmembrane transport and receptor activation. Additionally, tissue-specific protein domains show enrichments in DNA-related functions. This confirms that receptor-activated signaling processes and transcriptional regulation are two key factors for tissue specificity. Furthermore, many protein complexes are widely expressed regardless of their size, and their formation is frequently controlled by very few tissue-specific proteins. Interestingly, the number of alternative transcripts is increased for widely expressed genes. This suggests that alternative splicing plays a prominent role in generating specific functional characteristics of tissues.
组织特异性基因表达可能导致某些蛋白质相互作用和复合物的存在或缺失，从而导致组织之间生物过程的功能差异很大。在这项研究中，我们整合了基于 RNA 测序的人类基因表达数据与蛋白质相互作用、结构域和复合物，以分析其组织特异性的功能意义。这表明组织特异性的特征是蛋白质、结构域、相互作用和复合物的数量比以前认为的要少得多。与以前的微阵列研究相比，我们基于 RNA 测序的分析表明，组织特异性的蛋白质相互作用不太常见，主要涉及跨膜运输和受体激活。此外，组织特异性蛋白质结构域在与 DNA 相关的功能上表现出富集。这证实了受体激活的信号转导过程和转录调控是组织特异性的两个关键因素。此外，许多蛋白质复合物广泛表达，而不管其大小如何，其形成通常由极少数组织特异性蛋白质控制。有趣的是，广泛表达的基因的可变剪接转录本数量增加。这表明可变剪接在产生组织特异性功能特征方面起着重要作用。
