TissueNet

Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs. TissueNet v.2 is an updated version of the TissueNet database previously featured in NAR. It includes over 40 human tissues profiled via RNA-sequencing or protein-based assays. Users can select their preferred expression data source and interactively set the expression threshold for determining tissue-association. The output of TissueNet v.2 underlines qualitative and quantitative features of query proteins and their PPIs. The tissue-specificity view highlights tissue-specific and globally-expressed proteins, and the quantitative view highlights proteins that were differentially expressed in the selected tissue relative to all other tissues. Together, these views allow users to quickly assess the unique versus global functionality of query proteins. Thus, TissueNet v.2 offers an extensive, quantitative and user-friendly interface to study the roles of human proteins across tissues.

解析人体蛋白质在组织内的分子互作，对于明确其组织特异性功能、阐明组织表型具有重要意义。然而，当前多数蛋白质-蛋白质相互作用（protein-protein interaction, PPI）尚未明确其对应的组织背景。TissueNet数据库正是为填补这一研究空白而开发，它将实验验证得到的PPI与同时表达该互作对两个蛋白的人体组织进行关联。用户可选择目标蛋白与组织，获取该查询蛋白及其组织关联PPI的互作网络视图。TissueNet v.2是此前发表于《NAR》的原版TissueNet数据库的更新版本。该数据库涵盖通过RNA测序（RNA-sequencing）或基于蛋白质的检测实验得到的40余种人体组织的表达谱数据。用户可自行选择偏好的表达数据源，并可交互式设置用于判定组织关联性的表达阈值。TissueNet v.2的分析结果可凸显查询蛋白及其PPI的定性与定量特征：组织特异性视图可突出显示组织特异性蛋白与全局表达蛋白，而定量视图则可展示相较于其余所有组织，目标组织中差异表达的蛋白。结合两类可视化视图，用户可快速评估查询蛋白的组织特异性功能与全局性功能差异。综上，TissueNet v.2提供了一套全面、定量且操作友好的交互平台，助力研究人员探究人体蛋白质在不同组织中的功能角色。

搜集汇总

背景与挑战

背景概述

TissueNet v.3是一个数据库，专注于收录成人和胚胎人类组织中蛋白质相互作用的实验数据。它提供交互式界面，允许用户根据组织表达数据筛选和可视化蛋白质相互作用网络，以支持组织特异性功能研究。该数据库基于RNA测序和蛋白质表达数据，帮助用户定量分析蛋白质在不同组织中的表达差异。