OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft

• Published in: Nucleic acids research 2024-10, Vol.53 (D1), p.D504-D515
• Main Authors: Zhang, Yintao, Lian, Xichen, Xu, Hangwei, Zhu, Sisi, Zhang, Hao, Ni, Ziheng, Fu, Tingting, Liu, Shuiping, Tao, Lin, Zhou, Ying, Zhu, Feng
• Format: Article
• Language: English
• Subjects: Database Issue
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae861

Patient-derived models (PDMs, particularly organoids and xenografts) are irreplaceable tools for precision medicine, from target development to lead identification, then to preclinical evaluation, and finally to clinical decision-making. So far, PDM-based proteomics has emerged to be one of the cutting-edge directions and massive data have been accumulated. However, such PDM-based proteomic data have not been provided by any of the available databases, and proteomics profiles of all proteins in proteomic study are also completely absent from existing databases. Herein, an integrated database named 'OrgXenomics' was thus developed to provide the proteomic data for PDMs, which was unique in (a) explicitly describing the establishment detail for a wide array of models, (b) systematically providing the proteomic profiles (expression/function/interaction) for all proteins in studied proteomic analysis and (c) comprehensively giving the raw data for diverse organoid/xenograft-based proteomic studies of various diseases. Our OrgXenomics was expected to server as one good complement to existing proteomic databases, and had great implication for the practice of precision medicine, which could be accessed at: https://idrblab.org/orgxenomics/.