{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:30Z","timestamp":1772138490440,"version":"3.50.1"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,9,9]],"date-time":"2021-09-09T00:00:00Z","timestamp":1631145600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R00 CA207871"],"award-info":[{"award-number":["R00 CA207871"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018154","name":"Innovation in Cancer Informatics","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018154","id-type":"DOI","asserted-by":"crossref"}]},{"name":"UPMC-ITTC"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01 AI141990"],"award-info":[{"award-number":["U01 AI141990"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CDC NIOSH","award":["2U24OH009077"],"award-info":[{"award-number":["2U24OH009077"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The identity and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. Recently single-cell technologies have been developed that enable simultaneous quantitative analysis of cell-surface receptor expression with transcriptional states.\u00a0To date,\u00a0these datasets have not been used to\u00a0systematically\u00a0develop\u00a0cell-context-specific maps of the interface between\u00a0signaling and transcriptional regulators\u00a0orchestrating cellular identity and function.\u00a0We present SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network), a computational method to link cell-surface receptors to transcription factors (TFs) by exploiting cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets with cis-regulatory information. SPaRTAN is applied to immune cell types in the blood to predict the coupling of signaling receptors with cell context-specific TFs. Selected predictions are validated by prior knowledge and flow cytometry analyses. SPaRTAN is then used to predict the signaling coupled TF states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN enhances the utility of CITE-seq datasets to uncover TF and cell-surface receptor relationships in diverse cellular states.<\/jats:p>","DOI":"10.1093\/nar\/gkab745","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T07:37:07Z","timestamp":1631086627000},"page":"9633-9647","source":"Crossref","is-referenced-by-count":15,"title":["SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators"],"prefix":"10.1093","volume":"49","author":[{"given":"Xiaojun","family":"Ma","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA\u00a015206, USA"},{"name":"UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashwin","family":"Somasundaram","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Hematology\/Oncology, University of Pittsburgh, Pittsburgh, PA\u00a015213, USA"},{"name":"UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zengbiao","family":"Qi","sequence":"additional","affiliation":[{"name":"UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas\u00a0J","family":"Hartman","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA\u00a015213, USA"},{"name":"UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6330-8526","authenticated-orcid":false,"given":"Harinder","family":"Singh","sequence":"additional","affiliation":[{"name":"Center for Systems Immunology and Department of Immunology, University of Pittsburgh, Pittsburgh, PA\u00a015213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3175-1777","authenticated-orcid":false,"given":"Hatice\u00a0Ulku","family":"Osmanbeyoglu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA\u00a015206, USA"},{"name":"Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA\u00a015261, USA"},{"name":"UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,9]]},"reference":[{"key":"2021092511333296500_B1","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nmeth.4380","article-title":"Simultaneous epitope and transcriptome measurement in single cells","volume":"14","author":"Stoeckius","year":"2017","journal-title":"Nat. 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J."},{"key":"2021092511333296500_B56","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nri3862","article-title":"Molecular and cellular insights into T cell exhaustion","volume":"15","author":"Wherry","year":"2015","journal-title":"Nat. Rev. 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