IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles
Summary: Recently, single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) have been developed to separately measure transcriptomes and chromatin accessibility profiles at the single-cell resolution. However, few methods can rel...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-11-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222016315 |
| _version_ | 1797989756652486656 |
|---|---|
| author | Junyao Jiang Pin Lyu Jinlian Li Sunan Huang Jiawang Tao Seth Blackshaw Jiang Qian Jie Wang |
| author_facet | Junyao Jiang Pin Lyu Jinlian Li Sunan Huang Jiawang Tao Seth Blackshaw Jiang Qian Jie Wang |
| author_sort | Junyao Jiang |
| collection | DOAJ |
| description | Summary: Recently, single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) have been developed to separately measure transcriptomes and chromatin accessibility profiles at the single-cell resolution. However, few methods can reliably integrate these data to perform regulatory network analysis. Here, we developed integrated regulatory network analysis (IReNA) for network inference through the integrated analysis of scRNA-seq and scATAC-seq data, network modularization, transcription factor enrichment, and construction of simplified intermodular regulatory networks. Using public datasets, we showed that integrated network analysis of scRNA-seq data with scATAC-seq data is more precise to identify known regulators than scRNA-seq data analysis alone. Moreover, IReNA outperformed currently available methods in identifying known regulators. IReNA facilitates the systems-level understanding of biological regulatory mechanisms and is available at https://github.com/jiang-junyao/IReNA. |
| first_indexed | 2024-04-11T08:24:29Z |
| format | Article |
| id | doaj.art-421d3b09adc0455c90bd9354749aaed3 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-11T08:24:29Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-421d3b09adc0455c90bd9354749aaed32022-12-22T04:34:48ZengElsevieriScience2589-00422022-11-012511105359IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profilesJunyao Jiang0Pin Lyu1Jinlian Li2Sunan Huang3Jiawang Tao4Seth Blackshaw5Jiang Qian6Jie Wang7CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, ChinaDepartment of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USACAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, ChinaCAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, ChinaCAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, ChinaSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USADepartment of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USACAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China; Corresponding authorSummary: Recently, single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) have been developed to separately measure transcriptomes and chromatin accessibility profiles at the single-cell resolution. However, few methods can reliably integrate these data to perform regulatory network analysis. Here, we developed integrated regulatory network analysis (IReNA) for network inference through the integrated analysis of scRNA-seq and scATAC-seq data, network modularization, transcription factor enrichment, and construction of simplified intermodular regulatory networks. Using public datasets, we showed that integrated network analysis of scRNA-seq data with scATAC-seq data is more precise to identify known regulators than scRNA-seq data analysis alone. Moreover, IReNA outperformed currently available methods in identifying known regulators. IReNA facilitates the systems-level understanding of biological regulatory mechanisms and is available at https://github.com/jiang-junyao/IReNA.http://www.sciencedirect.com/science/article/pii/S2589004222016315Biochemistrymolecular networktranscriptomics |
| spellingShingle | Junyao Jiang Pin Lyu Jinlian Li Sunan Huang Jiawang Tao Seth Blackshaw Jiang Qian Jie Wang IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles iScience Biochemistry molecular network transcriptomics |
| title | IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles |
| title_full | IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles |
| title_fullStr | IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles |
| title_full_unstemmed | IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles |
| title_short | IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles |
| title_sort | irena integrated regulatory network analysis of single cell transcriptomes and chromatin accessibility profiles |
| topic | Biochemistry molecular network transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222016315 |
| work_keys_str_mv | AT junyaojiang irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT pinlyu irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT jinlianli irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT sunanhuang irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT jiawangtao irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT sethblackshaw irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT jiangqian irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles AT jiewang irenaintegratedregulatorynetworkanalysisofsinglecelltranscriptomesandchromatinaccessibilityprofiles |