{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T04:07:03Z","timestamp":1777349223210,"version":"3.51.4"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,2,3]],"date-time":"2024-02-03T00:00:00Z","timestamp":1706918400000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFF1200901"],"award-info":[{"award-number":["2021YFF1200901"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62133006"],"award-info":[{"award-number":["62133006"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). Integrated 15 transcriptomic datasets of HCC clinical samples, the first version of HCC database (HCCDB v1.0) was released in 2018. Through the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets, it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. With four years having passed, the database now needs integration of recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric is proposed as well to summarize cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available at http:\/\/lifeome.net\/database\/hccdb2.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae011","type":"journal-article","created":{"date-parts":[[2024,2,4]],"date-time":"2024-02-04T00:16:42Z","timestamp":1707005802000},"source":"Crossref","is-referenced-by-count":22,"title":["HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4762-7516","authenticated-orcid":false,"given":"Ziming","family":"Jiang","sequence":"first","affiliation":[{"name":"Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100006, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1677-0467","authenticated-orcid":false,"given":"Yanhong","family":"Wu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Institute for Precision Medicine & Department of Automation, Tsinghua University , Beijing 100084, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1738-2466","authenticated-orcid":false,"given":"Yuxin","family":"Miao","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Institute for Precision Medicine & Department of Automation, Tsinghua University , Beijing 100084, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4461-1746","authenticated-orcid":false,"given":"Kaige","family":"Deng","sequence":"additional","affiliation":[{"name":"Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4978-6983","authenticated-orcid":false,"given":"Fan","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730, China"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-2519-3760","authenticated-orcid":false,"given":"Shuhuan","family":"Xu","sequence":"additional","affiliation":[{"name":"Fuzhou Institute for Data Technology , Fuzhou 350207, China"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5312-4334","authenticated-orcid":false,"given":"Yupeng","family":"Wang","sequence":"additional","affiliation":[{"name":"Fuzhou Institute for Data Technology , Fuzhou 350207, China"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6795-8864","authenticated-orcid":false,"given":"Renke","family":"You","sequence":"additional","affiliation":[{"name":"Fuzhou Institute for Data Technology , Fuzhou 350207, China"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0956-6935","authenticated-orcid":false,"given":"Lei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Fuzhou Institute for Data Technology , Fuzhou 350207, China"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-8290-8896","authenticated-orcid":false,"given":"Yuhan","family":"Fan","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Institute for Precision Medicine & Department of Automation, Tsinghua University , Beijing 100084, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7973-6795","authenticated-orcid":false,"given":"Wenbo","family":"Guo","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Institute for Precision Medicine & Department of Automation, Tsinghua University , Beijing 100084, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5279-1989","authenticated-orcid":false,"given":"Qiuyu","family":"Lian","sequence":"additional","affiliation":[{"name":"University of Michigan \u2013 Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University , Shanghai 200240, China"},{"name":"Department of Automation, Shanghai Jiao Tong University , Shanghai 200240, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9380-9559","authenticated-orcid":false,"given":"Lei","family":"Chen","sequence":"additional","affiliation":[{"name":"International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University , Shanghai 200438, China"},{"name":"National Center for Liver Cancer , Shanghai 201805, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9684-5643","authenticated-orcid":false,"given":"Xuegong","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Institute for Precision Medicine & Department of Automation, Tsinghua University , Beijing 100084, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5916-2392","authenticated-orcid":false,"given":"Yongchang","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100730, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3968-8036","authenticated-orcid":false,"given":"Jin","family":"Gu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Institute for Precision Medicine & Department of Automation, Tsinghua University , Beijing 100084, China"}]}],"member":"286","published-online":{"date-parts":[[2024,2,3]]},"reference":[{"key":"2024061801505990900_qzae011-B1","doi-asserted-by":"crossref","first-page":"394","DOI":"10.3322\/caac.21492","article-title":"Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"68","author":"Bray","year":"2018","journal-title":"CA Cancer J 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