{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:49:34Z","timestamp":1753876174190,"version":"3.41.2"},"reference-count":37,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T00:00:00Z","timestamp":1643932800000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics","award":["HNSZD202003, X.T."],"award-info":[{"award-number":["HNSZD202003, X.T."]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The characterization of subcellular protein localization provides a basis for further understanding cellular behaviors. A delineation of subcellular localization of proteins on cytosolic membrane-bound organelles in human liver cancer cell lines (hLCCLs) has yet to be performed. To obtain its proteome-wide view, we isolated and enriched six cytosolic membrane-bound organelles in one of the hLCCLs (SK_HEP1) and quantified their proteins using mass spectrometry. The vigorous selection of marker proteins and a machine-learning-based algorithm were implemented to localize proteins at cluster and neighborhood levels. We validated the performance of the proposed method by comparing the predicted subcellular protein localization with publicly available resources. The profiles enabled investigating the correlation of protein domains with their subcellular localization and colocalization of protein complex members. A subcellular proteome database for SK_HEP1, including (i) the subcellular protein localization and (ii) the subcellular locations of protein complex members and their interactions, was constructed. Our research provides resources for further research on hLCCLs proteomics.<\/jats:p>\n               <jats:p>Database URL: http:\/\/www.igenetics.org.cn\/project\/PSL-LCCL\/<\/jats:p>","DOI":"10.1093\/database\/baab087","type":"journal-article","created":{"date-parts":[[2021,12,31]],"date-time":"2021-12-31T20:10:46Z","timestamp":1640981446000},"source":"Crossref","is-referenced-by-count":5,"title":["PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1"],"prefix":"10.1093","volume":"2022","author":[{"given":"Fang","family":"Huang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xia","family":"Tang","sequence":"additional","affiliation":[{"name":"Medical Genetic Institute of Henan Province, Henan Provincial People\u2019s Hospital, Henan Key Laboratory of Genetic Disease and Functional Genomics, National Health Commission Key Laboratory of Birth Defect Prevention, Henan Provincial People\u2019s Hospital of Henan University, People\u2019s Hospital of Zhengzhou University, #7 Road Weiwu, Jinshui District, Zhengzhou, Henan 450003, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, #1 Road Yixueyuan, Yuzhong District, Chongqing 400016, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Songfeng","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, #38 life science park, Changping District, Beijing 102206, People\u2019s Republic of China"},{"name":"Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, #1 Road Yixueyuan, Yuzhong District, Chongqing 400016, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3496-6415","authenticated-orcid":false,"given":"Keyue","family":"Ding","sequence":"additional","affiliation":[{"name":"Medical Genetic Institute of Henan Province, Henan Provincial People\u2019s Hospital, Henan Key Laboratory of Genetic Disease and Functional Genomics, National Health Commission Key Laboratory of Birth Defect Prevention, Henan Provincial People\u2019s Hospital of Henan University, People\u2019s Hospital of Zhengzhou University, #7 Road Weiwu, Jinshui District, Zhengzhou, Henan 450003, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,1,17]]},"reference":[{"key":"2022041207171198200_R1","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41580-018-0094-y","article-title":"Spatial proteomics: a powerful discovery tool for cell biology","volume":"20","author":"Lundberg","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2022041207171198200_R2","doi-asserted-by":"crossref","DOI":"10.3390\/ijms21010318","article-title":"Differential subcellular distribution and translocation of seven 14-3-3 isoforms in response to EGF and during the cell cycle","volume":"21","author":"Abdrabou","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"2022041207171198200_R3","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1111\/tra.12310","article-title":"Mechanisms regulating protein localization","volume":"16","author":"Bauer","year":"2015","journal-title":"Traffic"},{"key":"2022041207171198200_R4","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1074\/mcp.M900429-MCP200","article-title":"A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage","volume":"9","author":"Boisvert","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2022041207171198200_R5","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.cels.2016.08.012","article-title":"A portrait of the human organelle proteome in space and time during cytomegalovirus infection","volume":"3","author":"Beltran","year":"2016","journal-title":"Cell Syst."},{"key":"2022041207171198200_R6","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.16950","article-title":"Global, quantitative and dynamic mapping of protein subcellular localization","volume":"5","author":"Itzhak","year":"2016","journal-title":"elife"},{"key":"2022041207171198200_R7","doi-asserted-by":"crossref","first-page":"2706","DOI":"10.1016\/j.celrep.2017.08.063","article-title":"A mass spectrometry-based approach for mapping protein subcellular localization reveals the spatial proteome of mouse primary neurons","volume":"20","author":"Itzhak","year":"2017","journal-title":"Cell Rep."},{"key":"2022041207171198200_R8","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.molcel.2018.11.035","article-title":"SubCellBarCode: proteome-wide mapping of protein localization and relocalization","volume":"73","author":"Orre","year":"2019","journal-title":"Mol. Cell"},{"key":"2022041207171198200_R9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-06172-7","article-title":"AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A","volume":"9","author":"Davies","year":"2018","journal-title":"Nat. Commun."},{"key":"2022041207171198200_R10","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1074\/mcp.M112.020230","article-title":"Protein correlation profiles identify lipid droplet proteins with high confidence","volume":"12","author":"Krahmer","year":"2013","journal-title":"Mol. Cell. Proteomics"},{"key":"2022041207171198200_R11","doi-asserted-by":"crossref","first-page":"3178","DOI":"10.1091\/mbc.e14-07-1198","article-title":"Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein\u2013protein interactions","volume":"25","author":"Borner","year":"2014","journal-title":"Mol. Biol. Cell"},{"key":"2022041207171198200_R12","doi-asserted-by":"crossref","first-page":"2836","DOI":"10.1016\/j.celrep.2017.06.014","article-title":"Definition of a high-confidence mitochondrial proteome at quantitative scale","volume":"19","author":"Morgenstern","year":"2017","journal-title":"Cell Rep."},{"key":"2022041207171198200_R13","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2019.02708","article-title":"TcellSubC: an atlas of the subcellular proteome of human t cells","volume":"10","author":"Joshi","year":"2019","journal-title":"Front Immunol."},{"key":"2022041207171198200_R14","doi-asserted-by":"crossref","first-page":"pl2","DOI":"10.1126\/scisignal.2002373","article-title":"A method to separate nuclear, cytosolic, and membrane-associated signaling molecules in cultured cells","volume":"4","author":"Liu","year":"2011","journal-title":"Sci. Signal."},{"key":"2022041207171198200_R15","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3322\/caac.21660","article-title":"Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"71","author":"Sung","year":"2021","journal-title":"CA Cancer J. Clin."},{"key":"2022041207171198200_R16","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2022041207171198200_R17","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.ccell.2019.07.001","article-title":"A pharmacogenomic landscape in human liver cancers","volume":"36","author":"Qiu","year":"2019","journal-title":"Cancer Cell"},{"key":"2022041207171198200_R18","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41586-019-0987-8","article-title":"Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma","volume":"567","author":"Jiang","year":"2019","journal-title":"Nature"},{"key":"2022041207171198200_R19","doi-asserted-by":"crossref","first-page":"3229","DOI":"10.1038\/s41388-020-1215-6","article-title":"DNA and RNA sequencing identified a novel oncogene VPS35 in liver hepatocellular carcinoma","volume":"39","author":"Zhang","year":"2020","journal-title":"Oncogene"},{"key":"2022041207171198200_R20","article-title":"Visualizing data using t-SNE","volume":"9","author":"Van der Maaten","year":"2008","journal-title":"J. Mach. Learn. Res."},{"key":"2022041207171198200_R21","doi-asserted-by":"crossref","DOI":"10.32614\/RJ-2016-021","article-title":"Mclust 5: clustering, classification and density estimation using gaussian finite mixture models","volume":"8","author":"Scrucca","year":"2016","journal-title":"R J."},{"key":"2022041207171198200_R22","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1038\/nmeth.3967","article-title":"MetaMass, a tool for meta-analysis of subcellular proteomics data","volume":"13","author":"Lund-Johansen","year":"2016","journal-title":"Nat. Methods"},{"key":"2022041207171198200_R23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-10-48","article-title":"GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists","volume":"10","author":"Eden","year":"2009","journal-title":"BMC Bioinform."},{"key":"2022041207171198200_R24","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The pfam protein families database: towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022041207171198200_R25","doi-asserted-by":"crossref","first-page":"D559","DOI":"10.1093\/nar\/gky973","article-title":"CORUM: the comprehensive resource of mammalian protein complexes\u20142019","volume":"47","author":"Giurgiu","year":"2019","journal-title":"Nucleic Acids Res."},{"volume-title":"Introduction to Multivariate Statistical Analysis in Chemometrics","year":"2009","author":"Varmuza","key":"2022041207171198200_R26"},{"key":"2022041207171198200_R27","doi-asserted-by":"crossref","DOI":"10.1126\/science.aal3321","article-title":"A subcellular map of the human proteome","volume":"356","author":"Thul","year":"2017","journal-title":"Science"},{"key":"2022041207171198200_R28","doi-asserted-by":"crossref","first-page":"D1541","DOI":"10.1093\/nar\/gkaa1011","article-title":"MitoCarta3. 0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations","volume":"49","author":"Rath","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022041207171198200_R29","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1002\/1873-3468.12329","article-title":"Mitochondrial transit peptide exhibits cell penetration ability and efficiently delivers macromolecules to mitochondria","volume":"590","author":"Jain","year":"2016","journal-title":"FEBS Lett."},{"key":"2022041207171198200_R30","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1016\/j.cell.2016.10.056","article-title":"Structural mechanism for cargo recognition by the retromer complex","volume":"167","author":"Lucas","year":"2016","journal-title":"Cell"},{"key":"2022041207171198200_R31","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/ncb2721","article-title":"A global analysis of SNX27\u2013retromer assembly and cargo specificity reveals a function in glucose and metal ion transport","volume":"15","author":"Steinberg","year":"2013","journal-title":"Nat. Cell Biol."},{"key":"2022041207171198200_R32","doi-asserted-by":"crossref","first-page":"D646","DOI":"10.1093\/nar\/gkm936","article-title":"CORUM: the comprehensive resource of mammalian protein complexes","volume":"36","author":"Ruepp","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2022041207171198200_R33","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1016\/j.bbrc.2008.02.150","article-title":"Identification of Tom5 and Tom6 in the preprotein translocase complex of human mitochondrial outer membrane","volume":"369","author":"Kato","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2022041207171198200_R34","doi-asserted-by":"crossref","first-page":"2136","DOI":"10.1074\/jbc.273.4.2136","article-title":"DNA-dependent protein kinase interacts with antigen receptor response element binding proteins NF90 and NF45","volume":"273","author":"Ting","year":"1998","journal-title":"J. Biol. Chem."},{"key":"2022041207171198200_R35","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab278","article-title":"PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection","volume":"22","author":"Ullah","year":"2021","journal-title":"Brief. Bioinform."},{"key":"2022041207171198200_R36","doi-asserted-by":"crossref","first-page":"1694","DOI":"10.1093\/oxfordjournals.molbev.a003957","article-title":"Scale-free behavior in protein domain networks","volume":"18","author":"Wuchty","year":"2001","journal-title":"Mol. Biol. Evol."},{"key":"2022041207171198200_R37","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.cell.2015.06.043","article-title":"The BioPlex network: a systematic exploration of the human interactome","volume":"162","author":"Huttlin","year":"2015","journal-title":"Cell"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baab087\/43365717\/baab087.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baab087\/43365717\/baab087.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T07:17:54Z","timestamp":1649747874000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baab087\/6521743"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,17]]},"references-count":37,"URL":"https:\/\/doi.org\/10.1093\/database\/baab087","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2022,2,1]]},"published":{"date-parts":[[2022,1,17]]},"article-number":"baab087"}}