Department of Computer Science, University of Pisa , Pisa , Italy.
Department of Clinical and Molecular Biomedicine, University of Catania , Catania , Italy.
Front Bioeng Biotechnol. 2015 May 8;3:58. doi: 10.3389/fbioe.2015.00058. eCollection 2015.
Protein-protein interaction (PPI) networks available in public repositories usually represent relationships between proteins within the cell. They ignore the specific set of tissues or tumors where the interactions take place. Indeed, proteins can form tissue-selective complexes, while they remain inactive in other tissues. For these reasons, a great attention has been recently paid to tissue-specific PPI networks, in which nodes are proteins of the global PPI network whose corresponding genes are preferentially expressed in specific tissues. In this paper, we present SPECTRA, a knowledge base to build and compare tissue or tumor-specific PPI networks. SPECTRA integrates gene expression and protein interaction data from the most authoritative online repositories. We also provide tools for visualizing and comparing such networks, in order to identify the expression and interaction changes of proteins across tissues, or between the normal and pathological states of the same tissue. SPECTRA is available as a web server at http://alpha.dmi.unict.it/spectra.
蛋白质-蛋白质相互作用 (PPI) 网络可在公共存储库中获得，这些网络通常代表细胞内蛋白质之间的关系。它们忽略了相互作用发生的特定组织或肿瘤。事实上，蛋白质可以形成组织选择性复合物，而在其他组织中它们保持不活跃。出于这些原因，最近人们对组织特异性 PPI 网络给予了极大的关注，其中节点是全局 PPI 网络中的蛋白质，其相应的基因在特定组织中优先表达。在本文中，我们提出了 SPECTRA，这是一个用于构建和比较组织或肿瘤特异性 PPI 网络的知识库。SPECTRA 整合了来自最权威在线存储库的基因表达和蛋白质相互作用数据。我们还提供了用于可视化和比较这些网络的工具，以便识别蛋白质在组织之间或同一组织的正常和病理状态之间的表达和相互作用变化。SPECTRA 可作为一个网络服务器在 http://alpha.dmi.unict.it/spectra 上使用。
