PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation

作者全名："Zhai, Zhaoyu; Zhang, Xuelu; Zhou, Lu; Lin, Zhewei; Kuang, Ni; Li, Qiang; Ma, Qinfeng; Tao, Haodong; Gao, Jieya; Ma, Shiyong; Pan, Jianbo"

作者地址："[Zhai, Zhaoyu; Zhang, Xuelu; Zhou, Lu; Lin, Zhewei; Kuang, Ni; Li, Qiang; Ma, Qinfeng; Tao, Haodong; Gao, Jieya; Ma, Shiyong; Pan, Jianbo] Chongqing Med Univ, Ctr Novel Target & Therapeut Intervent, Inst Life Sci, Chongqing 400016, Peoples R China"

通信作者："Pan, JB (通讯作者)，Chongqing Med Univ, Ctr Novel Target & Therapeut Intervent, Inst Life Sci, Chongqing 400016, Peoples R China."

来源：NUCLEIC ACIDS RESEARCH

ESI学科分类：BIOLOGY & BIOCHEMISTRY

WOS号：WOS:000868393600001

JCR分区：Q1

影响因子：14.9

年份：2022

卷号：　

期号：　

开始页：　

结束页：　

文献类型：Article; Early Access

关键词：　

摘要："Genetically modified organisms (GMOs) can be generated to model human genetic disease or plant disease resistance, and they have contributed to the exploration and understanding of gene function, physiology, disease onset and drug target discovery. Here, PertOrg (http://www.inbirg.com/pertorg/) was introduced to provide multilevel alterations in GMOs. Raw data of 58 707 transcriptome profiles and associated information, such as phenotypic alterations, were collected and curated from studies involving in vivo genetic perturbation (e.g. knockdown, knockout and overexpression) in eight model organisms, including mouse, rat and zebrafish. The transcriptome profiles from before and after perturbation were organized into 10 116 comparison datasets, including 122 single-cell RNA-seq datasets. The raw data were checked and analysed using widely accepted and standardized pipelines to identify differentially expressed genes (DEGs) in perturbed organisms. As a result, 8 644 148 DEGs were identified and deposited as signatures of gene perturbations. Downstream functional enrichment analysis, cell type analysis and phenotypic alterations were also provided when available. Multiple search methods and analytical tools were created and implemented. Furthermore, case studies were presented to demonstrate how users can utilize the database. PertOrg 1.0 will be a valuable resource aiding in the exploration of gene functions, biological processes and disease models."

基金机构：Chongqing Medical University; National Natural Science Foundation of China [82104063]; University Innovation Research Group Project of Chongqing [CXQT21016]

基金资助正文：Chongqing Medical University; National Natural Science Foundation of China [82104063]; University Innovation Research Group Project of Chongqing [CXQT21016]. Funding for open access charge: Chongqing Medical University.