Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National & Kapodistrian University of Athens, 15701 Athens, Greece.
Institute for Fundamental Biomedical Research, Biomedical Science Research Center "Alexander Fleming", Vari, 16672 Athens, Greece.
Biomolecules. 2023 Feb 1;13(2):270. doi: 10.3390/biom13020270.
Receptor tyrosine kinases (RTKs) form a highly important group of protein receptors of the eukaryotic cell membrane. They control many vital cellular functions and are involved in the regulation of complex signaling networks. Mutations in RTKs have been associated with different types of cancers and other diseases. Although they are very important for proper cell function, they have been experimentally studied in a limited range of eukaryotic species. Currently, there is no available database for RTKs providing information about their function, expression, and interactions. Therefore, the identification of RTKs in multiple organisms, the documentation of their characteristics, and the collection of related information would be very useful. In this paper, we present a novel RTK detection pipeline (RTK-PRED) and the Receptor Tyrosine Kinases Database (TyReK-DB). RTK-PRED combines profile HMMs with transmembrane topology prediction to identify and classify potential RTKs. Proteins of all eukaryotic reference proteomes of the UniProt database were used as input in RTK-PRED leading to a filtered dataset of 20,478 RTKs. Based on the information collected for these RTKs from multiple databases, the relational TyReK database was created.
受体酪氨酸激酶 (RTKs) 是真核细胞膜上高度重要的蛋白受体组。它们控制许多重要的细胞功能，并参与调节复杂的信号网络。RTKs 的突变与不同类型的癌症和其他疾病有关。尽管它们对细胞功能的正常发挥非常重要，但它们在实验上仅在有限的几种真核物种中进行了研究。目前，尚无提供有关 RTKs 功能、表达和相互作用信息的可用数据库。因此，鉴定多种生物体中的 RTKs、记录其特征并收集相关信息将非常有用。在本文中，我们提出了一种新的 RTK 检测管道 (RTK-PRED) 和受体酪氨酸激酶数据库 (TyReK-DB)。RTK-PRED 将轮廓 HMM 与跨膜拓扑预测相结合，以识别和分类潜在的 RTKs。将 UniProt 数据库中所有真核参考蛋白质组用作 RTK-PRED 的输入，从而得到 20,478 个 RTKs 的过滤数据集。基于从多个数据库中为这些 RTKs 收集的信息，创建了关系型 TyReK 数据库。
