ScMoresDB: A Comprehensive Database of Single-cell Multi-omics Data for Human Respiratory System

Overview

Journal iScience

Publisher Cell Press

Date 2024 Apr 15

PMID 38617561

Authors

Kang Chen

Yutong Han

Yanni Wang

Dingli Zhou

Fanjie Wu

Wenhao Cai

Shikang Zheng

Qinyuan Xiao

Haiyue Zhang

Weizhong Li

Affiliations

Soon will be listed here.

Abstract

The human respiratory system is a complex and important system that can suffer a variety of diseases. Single-cell sequencing technologies, applied in many respiratory disease studies, have enhanced our ability in characterizing molecular and phenotypic features at a single-cell resolution. The exponentially increasing data from these studies have consequently led to difficulties in data sharing and analysis. Here, we present scMoresDB, a single-cell multi-omics database platform with extensive omics types tailored for human respiratory diseases. scMoresDB re-analyzes single-cell multi-omics datasets, providing a user-friendly interface with cross-omics search capabilities, interactive visualizations, and analytical tools for comprehensive data sharing and integrative analysis. Our example applications highlight the potential significance of BSG receptor in SARS-CoV-2 infection as well as the involvement of HHIP and TGFB2 in the development and progression of chronic obstructive pulmonary disease. scMoresDB significantly increases accessibility and utility of single-cell data relevant to human respiratory system and associated diseases.

Citing Articles

Advances in modeling cellular state dynamics: integrating omics data and predictive techniques.

Jung S Anim Cells Syst (Seoul). 2025; 29(1):72-83.

PMID: 39807350 PMC: 11727055. DOI: 10.1080/19768354.2024.2449518.

References

Stuart T, Srivastava A, Madad S, Lareau C, Satija R . Single-cell chromatin state analysis with Signac. Nat Methods. 2021; 18(11):1333-1341. PMC: 9255697. DOI: 10.1038/s41592-021-01282-5. View

Cusanovich D, Hill A, Aghamirzaie D, Daza R, Pliner H, Berletch J . A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell. 2018; 174(5):1309-1324.e18. PMC: 6158300. DOI: 10.1016/j.cell.2018.06.052. View

Borcherding N, Bormann N, Kraus G . scRepertoire: An R-based toolkit for single-cell immune receptor analysis. F1000Res. 2020; 9:47. PMC: 7400693. DOI: 10.12688/f1000research.22139.2. View

Barrett T, Wilhite S, Ledoux P, Evangelista C, Kim I, Tomashevsky M . NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2012; 41(Database issue):D991-5. PMC: 3531084. DOI: 10.1093/nar/gks1193. View

Wang J, Huang D, Zhou Y, Yao H, Liu H, Zhai S . CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies. Nucleic Acids Res. 2019; 48(D1):D807-D816. PMC: 7145620. DOI: 10.1093/nar/gkz1026. View

Parker M, Hao Y, Guo F, Pham B, Chase R, Platig J . Identification of an emphysema-associated genetic variant near with regulatory effects in lung fibroblasts. Elife. 2019; 8. PMC: 6693893. DOI: 10.7554/eLife.42720. View

Whitsett J, Wert S, Weaver T . Alveolar surfactant homeostasis and the pathogenesis of pulmonary disease. Annu Rev Med. 2009; 61:105-19. PMC: 4127631. DOI: 10.1146/annurev.med.60.041807.123500. View

Christenson S, Smith B, Bafadhel M, Putcha N . Chronic obstructive pulmonary disease. Lancet. 2022; 399(10342):2227-2242. DOI: 10.1016/S0140-6736(22)00470-6. View

Kan M, Diwadkar A, Saxena S, Shuai H, Joo J, Himes B . REALGAR: a web app of integrated respiratory omics data. Bioinformatics. 2022; 38(18):4442-4445. PMC: 9477519. DOI: 10.1093/bioinformatics/btac524. View

10.

Sakornsakolpat P, Prokopenko D, Lamontagne M, Reeve N, Guyatt A, Jackson V . Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations. Nat Genet. 2019; 51(3):494-505. PMC: 6546635. DOI: 10.1038/s41588-018-0342-2. View

11.

Tlemsani C, Pongor L, Elloumi F, Girard L, Huffman K, Roper N . SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures. Cell Rep. 2020; 33(3):108296. PMC: 7643325. DOI: 10.1016/j.celrep.2020.108296. View

12.

Gaddis N, Fortriede J, Guo M, Bardes E, Kouril M, Tabar S . LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. Am J Respir Cell Mol Biol. 2022; 70(2):129-139. PMC: 10848697. DOI: 10.1165/rcmb.2022-0165OC. View

13.

Carlier F, De Fays C, Pilette C . Epithelial Barrier Dysfunction in Chronic Respiratory Diseases. Front Physiol. 2021; 12:691227. PMC: 8264588. DOI: 10.3389/fphys.2021.691227. View

14.

Du Y, Kitzmiller J, Sridharan A, Perl A, Bridges J, Misra R . Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development. Thorax. 2017; 72(5):481-484. PMC: 5520249. DOI: 10.1136/thoraxjnl-2016-209598. View

15.

Cao Y, Su B, Guo X, Sun W, Deng Y, Bao L . Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells. Cell. 2020; 182(1):73-84.e16. PMC: 7231725. DOI: 10.1016/j.cell.2020.05.025. View

16.

Goedhart J, Luijsterburg M . VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots. Sci Rep. 2020; 10(1):20560. PMC: 7689420. DOI: 10.1038/s41598-020-76603-3. View

17.

Sarkans U, Fullgrabe A, Ali A, Athar A, Behrangi E, Diaz N . From ArrayExpress to BioStudies. Nucleic Acids Res. 2020; 49(D1):D1502-D1506. PMC: 7778911. DOI: 10.1093/nar/gkaa1062. View

18.

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J . A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020; 382(8):727-733. PMC: 7092803. DOI: 10.1056/NEJMoa2001017. View

19.

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay P, Swerdlow H . Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 2017; 14(9):865-868. PMC: 5669064. DOI: 10.1038/nmeth.4380. View

20.

Zhao T, Lyu S, Lu G, Juan L, Zeng X, Wei Z . SC2disease: a manually curated database of single-cell transcriptome for human diseases. Nucleic Acids Res. 2020; 49(D1):D1413-D1419. PMC: 7778914. DOI: 10.1093/nar/gkaa838. View