{"title":"scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies.","authors":"Jialin Mai,Qiheng Qian,Hao Gao,Zhuojing Fan,Jingyao Zeng,Jingfa Xiao","doi":"10.1093/nar/gkae931","DOIUrl":null,"url":null,"abstract":"Single-cell transcriptome-wide association studies (scTWAS) is a new method for conducting TWAS analysis at the cellular level to identify gene-trait associations with higher precision. This approach helps overcome the challenge of interpreting cell-type heterogeneity in traditional TWAS results. As the field of scTWAS rapidly advances, there is a growing need for additional database platforms to integrate this wealth of data and knowledge effectively. To address this gap, we present scTWAS Atlas (https://ngdc.cncb.ac.cn/sctwas/), a comprehensive database of scTWAS information integrating literature curation and data analysis. The current version of scTWAS Atlas amasses 2,765,211 associations encompassing 34 traits, 30 cell types, 9 cell conditions and 16,470 genes. The database features visualization tools, including an interactive knowledge graph that integrates single-cell expression quantitative trait loci (sc-eQTL) and scTWAS associations to build a multi-omics level regulatory network at the cellular level. Additionally, scTWAS Atlas facilitates cross-cell-type analysis, highlighting cell-type-specific and shared TWAS genes. The database is designed with user-friendly interfaces and allows for easy browsing, searching, and downloading of relevant information. Overall, scTWAS Atlas is instrumental in exploring the genetic regulatory mechanisms at the cellular level and shedding light on the role of various cell types in biological processes, offering novel insights for human health research.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":null,"pages":null},"PeriodicalIF":16.6000,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nucleic Acids Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/nar/gkae931","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Single-cell transcriptome-wide association studies (scTWAS) is a new method for conducting TWAS analysis at the cellular level to identify gene-trait associations with higher precision. This approach helps overcome the challenge of interpreting cell-type heterogeneity in traditional TWAS results. As the field of scTWAS rapidly advances, there is a growing need for additional database platforms to integrate this wealth of data and knowledge effectively. To address this gap, we present scTWAS Atlas (https://ngdc.cncb.ac.cn/sctwas/), a comprehensive database of scTWAS information integrating literature curation and data analysis. The current version of scTWAS Atlas amasses 2,765,211 associations encompassing 34 traits, 30 cell types, 9 cell conditions and 16,470 genes. The database features visualization tools, including an interactive knowledge graph that integrates single-cell expression quantitative trait loci (sc-eQTL) and scTWAS associations to build a multi-omics level regulatory network at the cellular level. Additionally, scTWAS Atlas facilitates cross-cell-type analysis, highlighting cell-type-specific and shared TWAS genes. The database is designed with user-friendly interfaces and allows for easy browsing, searching, and downloading of relevant information. Overall, scTWAS Atlas is instrumental in exploring the genetic regulatory mechanisms at the cellular level and shedding light on the role of various cell types in biological processes, offering novel insights for human health research.
期刊介绍:
Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.