{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T20:19:20Z","timestamp":1774383560659,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,5,21]],"date-time":"2020-05-21T00:00:00Z","timestamp":1590019200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61903277"],"award-info":[{"award-number":["61903277"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61871294"],"award-info":[{"award-number":["61871294"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61873193"],"award-info":[{"award-number":["61873193"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61773346"],"award-info":[{"award-number":["61773346"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61902352"],"award-info":[{"award-number":["61902352"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science Foundation of Zhejiang Province","award":["LR19C060001"],"award-info":[{"award-number":["LR19C060001"]}]},{"name":"Science Foundation of Zhejiang Province","award":["LZ20F030002"],"award-info":[{"award-number":["LZ20F030002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>At present, a fundamental challenge in single-cell RNA-sequencing data analysis is functional interpretation and annotation of cell clusters. Biological pathways in distinct cell types have different activation patterns, which facilitates the understanding of cell functions using single-cell transcriptomics. However, no effective web tool has been implemented for single-cell transcriptome data analysis based on prior biological pathway knowledge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present scTPA, a web-based platform for pathway-based analysis of single-cell RNA-seq data in human and mouse. scTPA incorporates four widely-used gene set enrichment methods to estimate the pathway activation scores of single cells based on a collection of available biological pathways with different functional and taxonomic classifications. The clustering analysis and cell-type-specific activation pathway identification were provided for the functional interpretation of cell types from a pathway-oriented perspective. An intuitive interface allows users to conveniently visualize and download single-cell pathway signatures. Overall, scTPA is a comprehensive tool for the identification of pathway activation signatures for the analysis of single cell heterogeneity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>http:\/\/sctpa.bio-data.cn\/sctpa.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>sujz@wmu.edu.cn or yufulong421@gmail.com or zgj@zjut.edu.cn<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa532","type":"journal-article","created":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T18:25:30Z","timestamp":1589567130000},"page":"4217-4219","source":"Crossref","is-referenced-by-count":26,"title":["scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures"],"prefix":"10.1093","volume":"36","author":[{"given":"Yan","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]},{"given":"Yaru","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9202-7515","authenticated-orcid":false,"given":"Jun","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023, Zhejiang, China"}]},{"given":"Ji","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]},{"given":"Fangjie","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]},{"given":"Meng","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7815-5884","authenticated-orcid":false,"given":"Guijun","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023, Zhejiang, China"}]},{"given":"Fulong","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]},{"given":"Jianzhong","family":"Su","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University , Wenzhou 325011, Zhejiang, China"}]}],"member":"286","published-online":{"date-parts":[[2020,5,21]]},"reference":[{"key":"2023062213540850700_btaa532-B1","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. 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