{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:31Z","timestamp":1772138011483,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,8,9]],"date-time":"2021-08-09T00:00:00Z","timestamp":1628467200000},"content-version":"vor","delay-in-days":102,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai","doi-asserted-by":"publisher","award":["JCYJ20190808150009605"],"award-info":[{"award-number":["JCYJ20190808150009605"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Project of China","award":["2016YFA0502201"],"award-info":[{"award-number":["2016YFA0502201"]}]},{"name":"National Key Project of China","award":["2017YFA0700404"],"award-info":[{"award-number":["2017YFA0700404"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Recent advances in bioinformatics analyses have led to the development of novel tools enabling the capture and trajectory mapping of single-cell RNA sequencing (scRNAseq) data. However, there is a lack of methods to assess the contributions of biological pathways and transcription factors to an overall developmental trajectory mapped from scRNAseq data. In this manuscript, we present a simplified approach for trajectory inference of pathway significance (TIPS) that leverages existing knowledgebases of functional pathways and other gene lists to provide further mechanistic insights into a biological process. TIPS identifies key pathways which contribute to a process of interest, as well as the individual genes that best reflect these changes. TIPS also provides insight into the relative timing of pathway changes, as well as a suite of visualizations to enable simplified data interpretation of scRNAseq libraries generated using a wide range of techniques. The TIPS package can be run through either a web server or downloaded as a user-friendly GUI run in R, and may serve as a useful tool to help biologists perform deeper functional analyses and visualization of their single-cell data.<\/jats:p>","DOI":"10.1093\/bib\/bbab124","type":"journal-article","created":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T16:13:06Z","timestamp":1616083986000},"source":"Crossref","is-referenced-by-count":12,"title":["TIPS: trajectory inference of pathway significance through pseudotime comparison for functional assessment of single-cell RNAseq data"],"prefix":"10.1093","volume":"22","author":[{"given":"Zihan","family":"Zheng","sequence":"first","affiliation":[{"name":"Biowavelet Ltd., Chongqing, China"},{"name":"Chongqing International Institute for Immunology, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Qiu","sequence":"additional","affiliation":[{"name":"R&D Department, TCRCure Ltd., Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiyang","family":"Wu","sequence":"additional","affiliation":[{"name":"R&D Department, TCRCure Ltd., Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Immunology, Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangyu","family":"Tang","sequence":"additional","affiliation":[{"name":"Biomedical Analysis Center, Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liyun","family":"Zou","sequence":"additional","affiliation":[{"name":"Department of Immunology, Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingyi","family":"Li","sequence":"additional","affiliation":[{"name":"Chongqing International Institute for Immunology, Chongqing, China"},{"name":"Department of Rheumatology and Immunology, First Affiliated Hospital of Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuzhang","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Immunology, Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianzhi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Biowavelet Ltd., Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shan","family":"Jiang","sequence":"additional","affiliation":[{"name":"Institute for Advanced Study, Shenzhen University, Shenzhen, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Wan","sequence":"additional","affiliation":[{"name":"Biomedical Analysis Center, Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingshan","family":"Ni","sequence":"additional","affiliation":[{"name":"Biomedical Analysis Center, Army Medical University, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,4,29]]},"reference":[{"issue":"11","key":"2021090815222766900_ref1","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat Methods"},{"issue":"7719","key":"2021090815222766900_ref2","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"la Manno","year":"2018","journal-title":"Nature"},{"issue":"4","key":"2021090815222766900_ref3","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat Protoc"},{"issue":"1","key":"2021090815222766900_ref4","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s13059-020-1926-6","article-title":"Eleven grand challenges in single-cell data science","volume":"21","author":"L\u00e4hnemann","year":"2020","journal-title":"Genome Biol"},{"key":"2021090815222766900_ref5","doi-asserted-by":"publisher","first-page":"1740","DOI":"10.12688\/f1000research.16613.2","article-title":"False signals induced by single-cell imputation. 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