{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,15]],"date-time":"2024-09-15T23:25:07Z","timestamp":1726442707848},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,1,9]],"date-time":"2023-01-09T00:00:00Z","timestamp":1673222400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,1,9]],"date-time":"2023-01-09T00:00:00Z","timestamp":1673222400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["62171236 and 61771251"],"award-info":[{"award-number":["62171236 and 61771251"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the key project of social development in Jiangsu Province","award":["BE2022799"],"award-info":[{"award-number":["BE2022799"]}]},{"name":"the key projects of Natural Science Research in Universities of Jiangsu Province","award":["22KJA180006","22KJA180006"],"award-info":[{"award-number":["22KJA180006","22KJA180006"]}]},{"name":"Qinglan Project in Jiangsu Province"},{"name":"the Open Research Fund of State Key Laboratory of Bioelectronics, Southeast University","award":["SKLB2022-K03"],"award-info":[{"award-number":["SKLB2022-K03"]}]},{"name":"funding from Shandong Provincial Key Laboratory of Biophysics"},{"name":"the Priority Academic Program Development of Jiangsu Higher Education Institution"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Gallbladder carcinoma (GBC), an aggressive malignant tumor of the biliary system, is characterized by high cellular heterogeneity and poor prognosis. Fewer data have been reported in GBC than other common cancer types. Multi-omics data will contribute to the understanding of the molecular mechanisms of cancer, cancer diagnosis and prognosis. Herein, to provide better understanding of the molecular events in GBC pathogenesis, we developed GBCdb (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/tmliang.cn\/gbc\/\">http:\/\/tmliang.cn\/gbc\/<\/jats:ext-link>), a user-friendly interface for the query and browsing of GBC-associated genes and RNA interaction networks using published multi-omics data, which also included experimentally supported data from different molecular levels. GBCdb will help to elucidate the potential biological roles of different RNAs and allow for the exploration of RNA interactions in GBC. These resources will provide an opportunity for unraveling the potential molecular features of Gallbladder carcinoma.\n<\/jats:p>","DOI":"10.1186\/s12859-023-05133-2","type":"journal-article","created":{"date-parts":[[2023,1,9]],"date-time":"2023-01-09T16:04:41Z","timestamp":1673280281000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["GBCdb: RNA expression landscapes and ncRNA\u2013mRNA interactions in gallbladder carcinoma"],"prefix":"10.1186","volume":"24","author":[{"given":"Li","family":"Guo","sequence":"first","affiliation":[]},{"given":"Yangyang","family":"Xiang","sequence":"additional","affiliation":[]},{"given":"Yuyang","family":"Dou","sequence":"additional","affiliation":[]},{"given":"Zibo","family":"Yin","sequence":"additional","affiliation":[]},{"given":"Xinru","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Lihua","family":"Tang","sequence":"additional","affiliation":[]},{"given":"Jiafeng","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Tingming","family":"Liang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,1,9]]},"reference":[{"key":"5133_CR1","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1053\/ejso.2001.1175","volume":"28","author":"S Varshney","year":"2002","unstructured":"Varshney S, Butturini G, Gupta R. Incidental carcinoma of the gallbladder. Eur J Surg Oncol. 2002;28:4\u201310.","journal-title":"Eur J Surg Oncol"},{"key":"5133_CR2","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1038\/nrc1429","volume":"4","author":"II Wistuba","year":"2004","unstructured":"Wistuba II, Gazdar AF. Gallbladder cancer: lessons from a rare tumour. Nat Rev Cancer. 2004;4:695\u2013706.","journal-title":"Nat Rev Cancer"},{"key":"5133_CR3","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1002\/cam4.2679","volume":"9","author":"W Mao","year":"2020","unstructured":"Mao W, Deng F, Wang D, Gao L, Shi X. Treatment of advanced gallbladder cancer: a SEER-based study. Cancer Med. 2020;9:141\u201350.","journal-title":"Cancer Med"},{"key":"5133_CR4","first-page":"99","volume":"6","author":"R Hundal","year":"2014","unstructured":"Hundal R, Shaffer EA. Gallbladder cancer: epidemiology and outcome. Clin Epidemiol. 2014;6:99\u2013109.","journal-title":"Clin Epidemiol"},{"key":"5133_CR5","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1136\/gutjnl-2018-316039","volume":"68","author":"M Li","year":"2019","unstructured":"Li M, Liu F, Zhang F, Zhou W, Jiang X, Yang Y, et al. Genomic ERBB2\/ERBB3 mutations promote PD-L1-mediated immune escape in gallbladder cancer: a whole-exome sequencing analysis. Gut. 2019;68:1024\u201333.","journal-title":"Gut"},{"key":"5133_CR6","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/ng.3030","volume":"46","author":"M Li","year":"2014","unstructured":"Li M, Zhang Z, Li X, Ye J, Wu X, Tan Z, et al. Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway. Nat Genet. 2014;46:872\u20136.","journal-title":"Nat Genet"},{"key":"5133_CR7","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1016\/S1665-2681(19)32065-4","volume":"4","author":"M Moreno","year":"2005","unstructured":"Moreno M, Pimentel F, Gazdar AF, Wistuba II, Miquel JF. TP53 abnormalities are frequent and early events in the sequential pathogenesis of gallbladder carcinoma. Ann Hepatol. 2005;4:192\u20139.","journal-title":"Ann Hepatol"},{"key":"5133_CR8","doi-asserted-by":"crossref","unstructured":"Shukla SK, Singh G, Shahi KS, Bhuvan, Pant P. Genetic Changes of P(53) and Kras in Gallbladder Carcinoma in Kumaon Region of Uttarakhand. J Gastrointest Cancer. 2020;51:552\u20139.","DOI":"10.1007\/s12029-019-00283-0"},{"key":"5133_CR9","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1007\/s00428-019-02706-6","volume":"476","author":"T Albrecht","year":"2020","unstructured":"Albrecht T, Rausch M, Roessler S, Geissler V, Albrecht M, Halske C, et al. HER2 gene (ERBB2) amplification is a low-frequency driver with potential predictive value in gallbladder carcinoma. Virchows Arch. 2020;476:871\u201380.","journal-title":"Virchows Arch"},{"key":"5133_CR10","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1159\/000366328","volume":"34","author":"G Zhu","year":"2014","unstructured":"Zhu G, Chen X, Wang X, Li X, Du Q, Hong H, et al. Expression of the RIP-1 gene and its role in growth and invasion of human gallbladder carcinoma. Cell Physiol Biochem. 2014;34:1152\u201365.","journal-title":"Cell Physiol Biochem"},{"key":"5133_CR11","first-page":"1017","volume":"137","author":"EI Roa","year":"2009","unstructured":"Roa EI, Lantadilla HS, Ibacache SG. de Aretxabala UX [p53 and p27 gene expression in subserosal gallbladder carcinoma]. Rev Med Chil. 2009;137:1017\u201322.","journal-title":"Rev Med Chil"},{"key":"5133_CR12","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1080\/15384101.2021.1874694","volume":"20","author":"ZB Jiang","year":"2021","unstructured":"Jiang ZB, Ma BQ, Feng Z, Liu SG, Gao P, Yan HT. miR-365 inhibits the progression of gallbladder carcinoma and predicts the prognosis of Gallbladder carcinoma patients. Cell Cycle. 2021;20:308\u201319.","journal-title":"Cell Cycle"},{"key":"5133_CR13","doi-asserted-by":"publisher","first-page":"855","DOI":"10.3892\/ol.2021.13116","volume":"22","author":"Z Sui","year":"2021","unstructured":"Sui Z, Sui X. Long non-coding RNA TMPO-AS1 promotes cell proliferation, migration, invasion and epithelial-to-mesenchymal transition in gallbladder carcinoma by regulating the microRNA-1179\/E2F2 axis. Oncol Lett. 2021;22:855.","journal-title":"Oncol Lett"},{"key":"5133_CR14","doi-asserted-by":"publisher","first-page":"10691","DOI":"10.1080\/21655979.2022.2065951","volume":"13","author":"X Hu","year":"2022","unstructured":"Hu X, Zhang J, Bu J, Yang K, Xu S, Pan M, et al. MiR-4733-5p promotes gallbladder carcinoma progression via directly targeting kruppel like factor 7. Bioengineered. 2022;13:10691\u2013706.","journal-title":"Bioengineered"},{"key":"5133_CR15","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1080\/15384101.2022.2042775","volume":"21","author":"X Yan","year":"2022","unstructured":"Yan X, Yang P, Liu H, Zhao Y, Wu Z, Zhang B. miR-4461 inhibits the progression of Gallbladder carcinoma via regulating EGFR\/AKT signaling. Cell Cycle. 2022;21:1166\u201377.","journal-title":"Cell Cycle"},{"key":"5133_CR16","doi-asserted-by":"publisher","first-page":"4796","DOI":"10.1038\/s41598-019-40857-3","volume":"9","author":"B Goeppert","year":"2019","unstructured":"Goeppert B, Truckenmueller F, Ori A, Fritz V, Albrecht T, Fraas A, et al. Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p. Sci Rep. 2019;9:4796.","journal-title":"Sci Rep"},{"key":"5133_CR17","first-page":"649","volume":"22","author":"SY Park","year":"2009","unstructured":"Park SY, Roh SJ, Kim YN, Kim SZ, Park HS, Jang KY, et al. Expression of MUC1, MUC2, MUC5AC and MUC6 in cholangiocarcinoma: prognostic impact. Oncol Rep. 2009;22:649\u201357.","journal-title":"Oncol Rep"},{"key":"5133_CR18","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/modpathol.3800762","volume":"20","author":"SH Li","year":"2007","unstructured":"Li SH, Li CF, Sung MT, Eng HL, Hsiung CY, Huang WW, et al. Skp2 is an independent prognosticator of gallbladder carcinoma among p27(Kip1)-interacting cell cycle regulators: an immunohistochemical study of 62 cases by tissue microarray. Mod Pathol. 2007;20:497\u2013507.","journal-title":"Mod Pathol"},{"key":"5133_CR19","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.462","volume":"11","author":"P Chen","year":"2021","unstructured":"Chen P, Wang Y, Li J, Bo X, Wang J, Nan L, et al. Diversity and intratumoral heterogeneity in human gallbladder cancer progression revealed by single-cell RNA sequencing. Clin Transl Med. 2021;11: e462.","journal-title":"Clin Transl Med"},{"key":"5133_CR20","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.683725","volume":"11","author":"Y Qin","year":"2021","unstructured":"Qin Y, Zheng Y, Huang C, Li Y, Gu M, Wu Q. Downregulation of miR-181b-5p inhibits the viability, migration, and glycolysis of gallbladder cancer by upregulating PDHX under hypoxia. Front Oncol. 2021;11: 683725.","journal-title":"Front Oncol"},{"key":"5133_CR21","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.201","volume":"10","author":"H Li","year":"2020","unstructured":"Li H, Hu Y, Jin Y, Zhu Y, Hao Y, Liu F, et al. Long noncoding RNA lncGALM increases risk of liver metastasis in gallbladder cancer through facilitating N-cadherin and IL-1beta-dependent liver arrest and tumor extravasation. Clin Transl Med. 2020;10: e201.","journal-title":"Clin Transl Med"},{"key":"5133_CR22","doi-asserted-by":"publisher","first-page":"1837","DOI":"10.15252\/embr.201744147","volume":"18","author":"XS Wu","year":"2017","unstructured":"Wu XS, Wang F, Li HF, Hu YP, Jiang L, Zhang F, et al. LncRNA-PAGBC acts as a microRNA sponge and promotes gallbladder tumorigenesis. EMBO Rep. 2017;18:1837\u201353.","journal-title":"EMBO Rep"},{"key":"5133_CR23","doi-asserted-by":"publisher","first-page":"5492","DOI":"10.1038\/s41467-019-13420-x","volume":"10","author":"S Xu","year":"2019","unstructured":"Xu S, Zhan M, Jiang C, He M, Yang L, Shen H, et al. Genome-wide CRISPR screen identifies ELP5 as a determinant of gemcitabine sensitivity in gallbladder cancer. Nat Commun. 2019;10:5492.","journal-title":"Nat Commun"},{"key":"5133_CR24","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1186\/s12943-019-1078-z","volume":"18","author":"S Wang","year":"2019","unstructured":"Wang S, Zhang Y, Cai Q, Ma M, Jin LY, Weng M, et al. Circular RNA FOXP1 promotes tumor progression and Warburg effect in gallbladder cancer by regulating PKLR expression. Mol Cancer. 2019;18:145.","journal-title":"Mol Cancer"},{"key":"5133_CR25","doi-asserted-by":"crossref","unstructured":"Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42:D92\u20137.","DOI":"10.1093\/nar\/gkt1248"},{"key":"5133_CR26","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1080\/15476286.2019.1600395","volume":"16","author":"M Liu","year":"2019","unstructured":"Liu M, Wang Q, Shen J, Yang BB, Ding X. Circbank: a comprehensive database for circRNA with standard nomenclature. RNA Biol. 2019;16:899\u2013905.","journal-title":"RNA Biol"},{"key":"5133_CR27","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1093\/nar\/gkx1311","volume":"46","author":"Y Li","year":"2018","unstructured":"Li Y, Li L, Wang Z, Pan T, Sahni N, Jin X, et al. LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. Nucleic Acids Res. 2018;46:1113\u201323.","journal-title":"Nucleic Acids Res"},{"key":"5133_CR28","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.gpb.2019.09.006","volume":"18","author":"Q Zhang","year":"2020","unstructured":"Zhang Q, Liu W, Zhang HM, Xie GY, Miao YR, Xia M, et al. hTFtarget: a comprehensive database for regulations of human transcription factors and their targets. Genom Proteom Bioinf. 2020;18:120\u20138.","journal-title":"Genom Proteom Bioinf"},{"key":"5133_CR29","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"ME Ritchie","year":"2015","unstructured":"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43: e47.","journal-title":"Nucleic Acids Res"},{"key":"5133_CR30","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","volume":"28","author":"JT Leek","year":"2012","unstructured":"Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28:882\u20133.","journal-title":"Bioinformatics"},{"key":"5133_CR31","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44\u201357.","journal-title":"Nat Protoc"},{"key":"5133_CR32","first-page":"100141","volume":"2","author":"T Wu","year":"2021","unstructured":"Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb). 2021;2:100141.","journal-title":"Innovation (Camb)."},{"key":"5133_CR33","doi-asserted-by":"publisher","first-page":"3771","DOI":"10.1093\/bioinformatics\/bty411","volume":"34","author":"CJ Liu","year":"2018","unstructured":"Liu CJ, Hu FF, Xia MX, Han L, Zhang Q, Guo AY. GSCALite: a web server for gene set cancer analysis. Bioinformatics. 2018;34:3771\u20132.","journal-title":"Bioinformatics"},{"key":"5133_CR34","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498\u2013504.","journal-title":"Genome Res"},{"key":"5133_CR35","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","volume":"47","author":"D Szklarczyk","year":"2019","unstructured":"Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein\u2013protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607\u201313.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05133-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05133-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05133-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,9]],"date-time":"2023-01-09T16:05:09Z","timestamp":1673280309000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05133-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,9]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5133"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05133-2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2023,1,9]]},"assertion":[{"value":"14 November 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 January 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 January 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"12"}}