{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:11Z","timestamp":1772165471748,"version":"3.50.1"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T00:00:00Z","timestamp":1747094400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T00:00:00Z","timestamp":1747094400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-2150134"],"award-info":[{"award-number":["DMS-2150134"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF DMS-1764421"],"award-info":[{"award-number":["NSF DMS-1764421"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["SFARI 597491-RWC"],"award-info":[{"award-number":["SFARI 597491-RWC"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-025-06143-y","type":"journal-article","created":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T00:32:13Z","timestamp":1747096333000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Integrating genetic and gene expression data in network-based stratification analysis of cancers"],"prefix":"10.1186","volume":"26","author":[{"given":"Kenny","family":"Liou","sequence":"first","affiliation":[]},{"given":"Ji-Ping","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,5,13]]},"reference":[{"key":"6143_CR1","doi-asserted-by":"publisher","unstructured":"The International Cancer Genome Consortium. International network of cancer genome projects. Nature. 2010;464(7291):993\u20138. https:\/\/doi.org\/10.1038\/nature08987.","DOI":"10.1038\/nature08987"},{"key":"6143_CR2","doi-asserted-by":"publisher","unstructured":"The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609\u201315. https:\/\/doi.org\/10.1038\/nature10166.","DOI":"10.1038\/nature10166"},{"key":"6143_CR3","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.cancergen.2023.10.001","volume":"278\u2013279","author":"H Liu","year":"2023","unstructured":"Liu H, Tang T. Pan-cancer genetic analysis of disulfidptosis-related gene set. Cancer Genet. 2023;278\u2013279:91\u2013103. https:\/\/doi.org\/10.1016\/j.cancergen.2023.10.001.","journal-title":"Cancer Genet."},{"key":"6143_CR4","doi-asserted-by":"publisher","DOI":"10.3233\/CBM-240119","author":"AM Rasteh","year":"2025","unstructured":"Rasteh AM, Liu H, Wang P. Pan-cancer genetic profiles of mitotic DNA integrity checkpoint protein kinases. Cancer Biomark. 2025. https:\/\/doi.org\/10.3233\/CBM-240119.","journal-title":"Cancer Biomark"},{"issue":"5","key":"6143_CR5","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1007\/s10142-024-01443-7","volume":"24","author":"H Liu","year":"2024","unstructured":"Liu H, Weng J, Huang CL, Jackson AP. Is the voltage-gated sodium channel $$\\beta$$3 subunit (SCN3B) a biomarker for glioma? Funct Integr Genom. 2024;24(5):162. https:\/\/doi.org\/10.1007\/s10142-024-01443-7.","journal-title":"Funct Integr Genom"},{"key":"6143_CR6","doi-asserted-by":"publisher","first-page":"19055","DOI":"10.1038\/s41598-023-45774-0","volume":"13","author":"H Liu","year":"2023","unstructured":"Liu H, Tang T. MAPK signaling pathway-based glioma subtypes, machine-learning risk model, and key hub proteins identification. Sci Rep. 2023;13:19055. https:\/\/doi.org\/10.1038\/s41598-023-45774-0.","journal-title":"Sci Rep"},{"issue":"45","key":"6143_CR7","doi-asserted-by":"publisher","first-page":"5904","DOI":"10.1038\/onc.2008.271","volume":"27","author":"TL Whiteside","year":"2008","unstructured":"Whiteside TL. The tumor microenvironment and its role in promoting tumor growth. Oncogene. 2008;27(45):5904\u201312. https:\/\/doi.org\/10.1038\/onc.2008.271.","journal-title":"Oncogene"},{"issue":"10","key":"6143_CR8","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1038\/ncponc1178","volume":"5","author":"PA Konstantinopoulos","year":"2008","unstructured":"Konstantinopoulos PA, Spentzos D, Cannistra SA. Gene expression profiling in epithelial ovarian cancer. Nat Rev Clin Oncol. 2008;5(10):577\u201387. https:\/\/doi.org\/10.1038\/ncponc1178.","journal-title":"Nat Rev Clin Oncol"},{"issue":"9805","key":"6143_CR9","doi-asserted-by":"publisher","first-page":"1812","DOI":"10.1016\/S0140-6736(11)61539-0","volume":"378","author":"JS Reis-Filho","year":"2011","unstructured":"Reis-Filho JS, Pusztai L. Gene expression profiling in breast cancer: classification, prognostication, and prediction. Lancet. 2011;378(9805):1812\u201323. https:\/\/doi.org\/10.1016\/S0140-6736(11)61539-0.","journal-title":"Lancet"},{"issue":"7407","key":"6143_CR10","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1038\/nature11252","volume":"487","author":"The Cancer Genome Atlas Network","year":"2012","unstructured":"The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330\u20137. https:\/\/doi.org\/10.1038\/nature11252.","journal-title":"Nature"},{"issue":"3","key":"6143_CR11","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/j.semcancer.2012.02.011","volume":"22","author":"E Raspe","year":"2012","unstructured":"Raspe E. Gene expression profiling to dissect the complexity of cancer biology: pitfalls and promise. Semin Cancer Biol. 2012;22(3):250\u201360. https:\/\/doi.org\/10.1016\/j.semcancer.2012.02.011.","journal-title":"Semin Cancer Biol"},{"key":"6143_CR12","doi-asserted-by":"publisher","DOI":"10.1016\/j.genrep.2024.102042","volume":"37","author":"H Liu","year":"2024","unstructured":"Liu H, Guo Z, Wang P. Genetic expression in cancer research: challenges and complexity. Gene Rep. 2024;37: 102042. https:\/\/doi.org\/10.1016\/j.genrep.2024.102042.","journal-title":"Gene Rep"},{"issue":"1","key":"6143_CR13","doi-asserted-by":"publisher","first-page":"34","DOI":"10.7150\/jca.100922","volume":"16","author":"H Liu","year":"2025","unstructured":"Liu H, Li Y, Karsidag M, Tu T, Wang P. Technical and biological biases in bulk transcriptomic data mining for cancer research. J Cancer. 2025;16(1):34\u201343. https:\/\/doi.org\/10.7150\/jca.100922.","journal-title":"J Cancer"},{"key":"6143_CR14","doi-asserted-by":"publisher","DOI":"10.4061\/2009\/869093","volume":"2009","author":"JS Hamid","year":"2009","unstructured":"Hamid JS, Hu P, Roslin NM, Ling V, Greenwood C, Beyene J. Data integration in genetics and genomics: methods and challenges. Hum Genom Proteom. 2009;2009: 869093. https:\/\/doi.org\/10.4061\/2009\/869093.","journal-title":"Hum Genom Proteom"},{"key":"6143_CR15","doi-asserted-by":"publisher","first-page":"1030","DOI":"10.3389\/fonc.2020.01030","volume":"10","author":"G Nicora","year":"2020","unstructured":"Nicora G, Vitali F, Dagliati A, Geifman N, Bellazzi R. Integrated multi-omics analyses in oncology: a review of machine learning methods and tools. Front Oncol. 2020;10:1030. https:\/\/doi.org\/10.3389\/fonc.2020.01030.","journal-title":"Front Oncol"},{"key":"6143_CR16","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.neucom.2018.03.072","volume":"324","author":"G Yang","year":"2019","unstructured":"Yang G, Xuequn S, Zhanhuai L. Identification of cancer subtypes by integrating multiple types of transcriptomics data with deep learning in breast cancer. Neurocomputing. 2019;324:20\u201330. https:\/\/doi.org\/10.1016\/j.neucom.2018.03.072.","journal-title":"Neurocomputing"},{"issue":"11","key":"6143_CR17","doi-asserted-by":"publisher","first-page":"4245","DOI":"10.1073\/pnas.1208949110","volume":"110","author":"M Qianxing","year":"2013","unstructured":"Qianxing M, Xuequn S, Zhanhuai L. Pattern discovery and cancer gene identification in integrated cancer genomic data. PNAS. 2013;110(11):4245\u201350. https:\/\/doi.org\/10.1073\/pnas.1208949110.","journal-title":"PNAS"},{"key":"6143_CR18","doi-asserted-by":"publisher","first-page":"117793221989905","DOI":"10.1177\/1177932219899051","volume":"14","author":"I Subramanian","year":"2020","unstructured":"Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics data integration, interpretation, and its application. Bioinform Biol Insights. 2020;14:1177932219899051. https:\/\/doi.org\/10.1177\/1177932219899051.","journal-title":"Bioinform Biol Insights"},{"issue":"4","key":"6143_CR19","doi-asserted-by":"publisher","DOI":"10.1002\/mco2.315","volume":"4","author":"C Chen","year":"2023","unstructured":"Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, et al. Applications of multi-omics analysis in human diseases. Med Commun. 2023;4(4): e315. https:\/\/doi.org\/10.1002\/mco2.315.","journal-title":"Med Commun"},{"issue":"1","key":"6143_CR20","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1093\/carcin\/bgp261","volume":"31","author":"PK Kreeger","year":"2010","unstructured":"Kreeger PK, Lauffenburger DA. Cancer systems biology: a network modeling perspective. Carcinogenesis. 2010;31(1):2\u20138. https:\/\/doi.org\/10.1093\/carcin\/bgp261.","journal-title":"Carcinogenesis"},{"issue":"11","key":"6143_CR21","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1038\/nmeth.2651","volume":"10","author":"M Hofree","year":"2013","unstructured":"Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013;10(11):1108\u201315. https:\/\/doi.org\/10.1038\/nmeth.2651.","journal-title":"Nat Methods"},{"issue":"4","key":"6143_CR22","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1177\/0962280213481053","volume":"25","author":"L Kang","year":"2013","unstructured":"Kang L, Liu A, Tian L. Linear combination methods to improve diagnostic\/prognostic accuracy on future observations. Stat Methods Med Res. 2013;25(4):1359\u201380. https:\/\/doi.org\/10.1177\/0962280213481053.","journal-title":"Stat Methods Med Res"},{"issue":"4","key":"6143_CR23","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1093\/biostatistics\/4.4.523","volume":"4","author":"R Etzioni","year":"2003","unstructured":"Etzioni R, Kooperberg C, Pepe M, Smith R, Gann PH. Combining biomarkers to detect disease with application to prostate cancer. Biostatistics. 2003;4(4):523\u201338. https:\/\/doi.org\/10.1093\/biostatistics\/4.4.523.","journal-title":"Biostatistics"},{"issue":"424","key":"6143_CR24","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1080\/01621459.1993.10476417","volume":"88","author":"JQ Su","year":"1993","unstructured":"Su JQ, Liu JS. Linear combinations of multiple diagnostic markers. J Am Stat Assoc. 1993;88(424):1350\u20135. https:\/\/doi.org\/10.1080\/01621459.1993.10476417.","journal-title":"J Am Stat Assoc"},{"issue":"4","key":"6143_CR25","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1016\/j.cels.2018.03.001","volume":"6","author":"JK Huang","year":"2018","unstructured":"Huang JK, Carlin DE, Yu MK, Zhang W, Kresiburg JF, Tamayo P, et al. Systematic evaluation of molecular networks for discovery of disease genes. Cell Syst. 2018;6(4):484-95.e5. https:\/\/doi.org\/10.1016\/j.cels.2018.03.001.","journal-title":"Cell Syst"},{"key":"6143_CR26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1075","author":"SA Forbes","year":"2015","unstructured":"Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world\u2019s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015. https:\/\/doi.org\/10.1093\/nar\/gku1075.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"6143_CR27","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646\u201374. https:\/\/doi.org\/10.1016\/j.cell.2011.02.013.","journal-title":"Cell"},{"issue":"3","key":"6143_CR28","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1016\/j.cell.2016.06.017","volume":"166","author":"F Iorio","year":"2016","unstructured":"Iorio F, Knijnenburg TA, Vis DJ, Bignell G, Menden MP, Schubert M, et al. A landscape of pharmacogenomic interactions in cancer. Cell. 2016;166(3):740\u201354. https:\/\/doi.org\/10.1016\/j.cell.2016.06.017.","journal-title":"Cell"},{"issue":"6127","key":"6143_CR29","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1126\/science.1235122","volume":"339","author":"B Vogelstein","year":"2013","unstructured":"Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science. 2013;339(6127):1546\u201358. https:\/\/doi.org\/10.1126\/science.1235122.","journal-title":"Science"},{"issue":"16","key":"6143_CR30","doi-asserted-by":"publisher","first-page":"2859","DOI":"10.1093\/bioinformatics\/bty186","volume":"34","author":"JK Huang","year":"2018","unstructured":"Huang JK, Jia T, Carlin DE, Ideker T. pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018;34(16):2859\u201361. https:\/\/doi.org\/10.1093\/bioinformatics\/bty186.","journal-title":"Bioinformatics"},{"key":"6143_CR31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000641","author":"O Vanunu","year":"2010","unstructured":"Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R. Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol. 2010. https:\/\/doi.org\/10.1371\/journal.pcbi.1000641.","journal-title":"PLoS Comput Biol"},{"issue":"6755","key":"6143_CR32","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/44565","volume":"401","author":"DD Lee","year":"1999","unstructured":"Lee DD, Seung HS. Learning the parts of objects by non-negative matrix factorization. Nature. 1999;401(6755):788\u201391. https:\/\/doi.org\/10.1038\/44565.","journal-title":"Nature"},{"issue":"12","key":"6143_CR33","doi-asserted-by":"publisher","first-page":"4164","DOI":"10.1073\/pnas.0308531101","volume":"101","author":"JP Brunet","year":"2004","unstructured":"Brunet JP, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad. 2004;101(12):4164\u20139. https:\/\/doi.org\/10.1073\/pnas.0308531101.","journal-title":"Proc Natl Acad"},{"key":"6143_CR34","doi-asserted-by":"publisher","unstructured":"Cai et al. Non-negative matrix factorization on manifold. In: 8th IEEE international conference in data mining. 2008; Pisa, Italy. p. 63\u201372. https:\/\/doi.org\/10.1109\/ICDM.2008.57.","DOI":"10.1109\/ICDM.2008.57"},{"key":"6143_CR35","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-16-S7-S7","author":"X Zhong","year":"2015","unstructured":"Zhong X, Yang H, Zhao S, Shyr Y, Li B. Network-based stratification analysis of 13 major cancer types using mutations in panels of cancer genes. BMC Genom. 2015. https:\/\/doi.org\/10.1186\/1471-2164-16-S7-S7.","journal-title":"BMC Genom"},{"issue":"5","key":"6143_CR36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0177662","volume":"12","author":"Z He","year":"2017","unstructured":"He Z, Zhang J, Yuan X, Liu Z, Liu B, Tuo S, et al. Network based stratification of major cancers by integrating somatic mutation and gene expression data. PLoS One. 2017;12(5): e0177662. https:\/\/doi.org\/10.1371\/journal.pone.0177662.","journal-title":"PLoS One"},{"key":"6143_CR37","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1023\/A:1023949509487","volume":"52","author":"S Monti","year":"2003","unstructured":"Monti S, et al. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach Learn. 2003;52:91\u2013118. https:\/\/doi.org\/10.1023\/A:1023949509487.","journal-title":"Mach Learn"},{"key":"6143_CR38","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","volume":"20","author":"PJ Rousseeuw","year":"1987","unstructured":"Rousseeuw PJ. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Appl Comput Math. 1987;20:53\u201365. https:\/\/doi.org\/10.1016\/0377-0427(87)90125-7.","journal-title":"J Appl Comput Math"},{"key":"6143_CR39","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3389\/fninf.2014.00014","volume":"8","author":"A Abraham","year":"2014","unstructured":"Abraham A, Pedregosa F, Eickenberg M, Gervais P, Mueller A, Kossaifi J, et al. Machine learning for neuroimaging with scikit-learn. Front Neuroinform. 2014;8:14. https:\/\/doi.org\/10.3389\/fninf.2014.00014.","journal-title":"Front Neuroinform"},{"issue":"40","key":"6143_CR40","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.21105\/joss.01317","volume":"4","author":"C Davidson-Pilon","year":"2019","unstructured":"Davidson-Pilon C. Lifelines: survival analysis in Python. J Open Source Softw. 2019;4(40):1317. https:\/\/doi.org\/10.21105\/joss.01317.","journal-title":"J Open Source Softw"},{"key":"6143_CR41","doi-asserted-by":"publisher","first-page":"2676","DOI":"10.12688\/f1000research.8231.1","volume":"5","author":"S P\u00f6lsterl","year":"2016","unstructured":"P\u00f6lsterl S, Gupta P, Wang L, Conjeti S, Katouzian A, Navab N. Heterogeneous ensembles for predicting survival of metastatic castrate-resistant prostate cancer patients. F1000Research. 2016;5:2676. https:\/\/doi.org\/10.12688\/f1000research.8231.1.","journal-title":"F1000Research"},{"issue":"282","key":"6143_CR42","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1080\/01621459.1958.10501452","volume":"53","author":"EL Kaplan","year":"1958","unstructured":"Kaplan EL, Meier P. Nonparametric estimation from incomplete observations. J Am Stat Assoc. 1958;53(282):457\u201381. https:\/\/doi.org\/10.1080\/01621459.1958.10501452.","journal-title":"J Am Stat Assoc"},{"issue":"4","key":"6143_CR43","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1214\/aos\/1176345976","volume":"10","author":"PK Andersen","year":"1982","unstructured":"Andersen PK, Gill RD. Cox\u2019s regression model for counting processes: a large sample study. Ann Stat. 1982;10(4):1100\u201320. https:\/\/doi.org\/10.1214\/aos\/1176345976.","journal-title":"Ann Stat"},{"key":"6143_CR44","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1507","author":"A Colaprico","year":"2016","unstructured":"Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, et al. TCGAbiolinks: an R\/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 2016. https:\/\/doi.org\/10.1093\/nar\/gkv1507.","journal-title":"Nucleic Acids Res"},{"key":"6143_CR45","doi-asserted-by":"publisher","first-page":"1542","DOI":"10.12688\/f1000research.8923.2","volume":"5","author":"TC Silva","year":"2016","unstructured":"Silva TC, Colaprico A, Olsen C, D\u2019Angelo F, Bontempi G, Ceccarelli M, et al. TCGA Workflow: analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Research. 2016;5:1542. https:\/\/doi.org\/10.12688\/f1000research.8923.2.","journal-title":"F1000Research"},{"key":"6143_CR46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006701","author":"M Mounir","year":"2019","unstructured":"Mounir M, Lucchetta M, Silva TC, Olsen C, Bontempi G, Chen X, et al. New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx. PLoS Comput Biol. 2019. https:\/\/doi.org\/10.1371\/journal.pcbi.1006701.","journal-title":"PLoS Comput Biol"},{"key":"6143_CR47","doi-asserted-by":"publisher","unstructured":"The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7351):609\u201315. https:\/\/doi.org\/10.1038\/nature10166.","DOI":"10.1038\/nature10166"},{"key":"6143_CR48","doi-asserted-by":"publisher","unstructured":"The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014;507(7493):315\u201322. https:\/\/doi.org\/10.1038\/nature12965.","DOI":"10.1038\/nature12965"},{"issue":"7447","key":"6143_CR49","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/nature12113","volume":"497","author":"DA Levine","year":"2013","unstructured":"Levine DA. The cancer genome atlas research network. integrated genomic characterization of endometrial carcinoma. Nature. 2013;497(7447):67\u201373. https:\/\/doi.org\/10.1038\/nature12113.","journal-title":"Nature"},{"issue":"6","key":"6143_CR50","doi-asserted-by":"publisher","DOI":"10.1016\/j.xinn.2024.100722","volume":"5","author":"G Yu","year":"2024","unstructured":"Yu G. Thirteen years of clusterProfiler. Innovation. 2024;5(6): 100722. https:\/\/doi.org\/10.1016\/j.xinn.2024.100722.","journal-title":"Innovation"},{"issue":"3","key":"6143_CR51","doi-asserted-by":"publisher","DOI":"10.1016\/j.xinn.2021.100141","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. 2021;2(3): 100141. https:\/\/doi.org\/10.1016\/j.xinn.2021.100141.","journal-title":"Innovation"},{"issue":"1","key":"6143_CR52","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27\u201330. https:\/\/doi.org\/10.1093\/nar\/28.1.27.","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"6143_CR53","doi-asserted-by":"publisher","first-page":"11318","DOI":"10.1073\/pnas.201208798","volume":"98","author":"J Han","year":"2001","unstructured":"Han J, Flemington C, Houghton AB, Gu Z, Zambetti GP, Lutz RJ, et al. Expression of bbc3, a pro-apoptotic BH3-only gene, is regulated by diverse cell death and survival signals. PNAS. 2001;98(20):11318\u201323. https:\/\/doi.org\/10.1073\/pnas.201208798.","journal-title":"PNAS"},{"issue":"8","key":"6143_CR54","doi-asserted-by":"publisher","first-page":"737","DOI":"10.4161\/cbt.10.8.13417","volume":"10","author":"S Dingding","year":"2010","unstructured":"Dingding S, Grossman SR. Ubiquitin becomes ubiquitous in cancer. Cancer Biol Ther. 2010;10(8):737\u201347. https:\/\/doi.org\/10.4161\/cbt.10.8.13417.","journal-title":"Cancer Biol Ther"},{"issue":"4","key":"6143_CR55","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/s12935-020-01641-w","volume":"21","author":"H Huang","year":"2021","unstructured":"Huang H, Zhang J, Ling F, Huang Y, Yang M, Zhang Y, et al. Leptin receptor (LEPR) promotes proliferation, migration, and invasion and inhibits apoptosis in hepatocellular carcinoma by regulating ANXA7. Cancer Cell Int. 2021;21(4):4. https:\/\/doi.org\/10.1186\/s12935-020-01641-w.","journal-title":"Cancer Cell Int"},{"issue":"10","key":"6143_CR56","doi-asserted-by":"publisher","first-page":"1498","DOI":"10.3390\/biom13101498","volume":"13","author":"MA Alfaqih","year":"2023","unstructured":"Alfaqih MA, Elsalem L, Nusier M, Mhedat K, Khader Y, Ababneh E. Serum leptin receptor and the rs1137101 variant of the LEPR gene are associated with bladder cancer. Biomolecules. 2023;13(10):1498. https:\/\/doi.org\/10.3390\/biom13101498.","journal-title":"Biomolecules"},{"key":"6143_CR57","doi-asserted-by":"publisher","DOI":"10.1093\/annonc\/mdz413.061","author":"AI Kalinkin","year":"2019","unstructured":"Kalinkin AI, Nemtsova MV, Zaletaev DV, Sigin VO, Ignatova E, Kuznetsova EB, et al. Leukotriene B4 receptors abnormal gene expression is associated with either shorter or longer survival in breast cancer patients depending on the intrinsic tumour molecular subtype. Ann Oncol. 2019. https:\/\/doi.org\/10.1093\/annonc\/mdz413.061.","journal-title":"Ann Oncol"},{"key":"6143_CR58","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1186\/1471-2407-11-443","volume":"11","author":"M Labelle-Cote","year":"2011","unstructured":"Labelle-Cote M, Dusseault J, Salma I, Picard-Cloutier A, Siegel PM, Larose L. Nck2 promotes human melanoma cell proliferation, migration and invasion in vitro and primary melanoma-derived tumor growth in vivo. BMC Cancer. 2011;11:443. https:\/\/doi.org\/10.1186\/1471-2407-11-443.","journal-title":"BMC Cancer"},{"issue":"10","key":"6143_CR59","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1038\/s41388-021-01902-6","volume":"41","author":"R Williams","year":"2022","unstructured":"Williams R, Jobling S, Sims AH, Mou C, Wilkinson L, Collu GM, et al. Elevated EDAR signalling promotes mammary gland tumourigenesis with squamous metaplasia. Oncogene. 2022;41(10):1040\u20139. https:\/\/doi.org\/10.1038\/s41388-021-01902-6.","journal-title":"Oncogene"},{"issue":"5","key":"6143_CR60","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1136\/jim-2021-002282","volume":"70","author":"H Zhang","year":"2022","unstructured":"Zhang H, Wang M, Chen D, Luo C. Dual-specificity phosphatase 8 (DUSP8) induces drug resistance in breast cancer by regulating MAPK pathways. J Investig Med. 2022;70(5):1293\u2013300. https:\/\/doi.org\/10.1136\/jim-2021-002282.","journal-title":"J Investig Med"},{"issue":"2","key":"6143_CR61","doi-asserted-by":"publisher","first-page":"1178","DOI":"10.1038\/s41388-024-02969-7","volume":"43","author":"K Turkowski","year":"2024","unstructured":"Turkowski K, Herzberg F, G\u00fcnther S, Weigert A, Haselbauer T, Fink L, et al. miR-147b mediated suppression of DUSP8 promotes lung cancer progression. Oncogene. 2024;43(2):1178\u201389. https:\/\/doi.org\/10.1038\/s41388-024-02969-7.","journal-title":"Oncogene"},{"key":"6143_CR62","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/s13578-019-0329-4","volume":"9","author":"T Ding","year":"2019","unstructured":"Ding T, Zhou Y, Long R, Chen C, Zhao J, Cui P, et al. DUSP8 phosphatase: structure, functions, expression regulation and the role in human diseases. Cell Biosci. 2019;9:70. https:\/\/doi.org\/10.1186\/s13578-019-0329-4.","journal-title":"Cell Biosci"},{"key":"6143_CR63","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/s41392-024-01868-3","volume":"9","author":"M Yi","year":"2024","unstructured":"Yi M, Li T, Niu M, Zhang H, Wu Y, Wu K, et al. Targeting cytokine and chemokine signaling pathways for cancer therapy. Sig Transduct Target Ther. 2024;9:176. https:\/\/doi.org\/10.1038\/s41392-024-01868-3.","journal-title":"Sig Transduct Target Ther"},{"key":"6143_CR64","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/s40001-024-01711-z","volume":"29","author":"T Abdul-Rahman","year":"2024","unstructured":"Abdul-Rahman T, Ghosh S, Badar SM, Nazir A, Bamigbade GB, Aji N, et al. The paradoxical role of cytokines and chemokines at the tumor microenvironment: a comprehensive review. Eur J Med Res. 2024;29:124. https:\/\/doi.org\/10.1186\/s40001-024-01711-z.","journal-title":"Eur J Med Res"},{"key":"6143_CR65","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13048-019-0596-z","volume":"12","author":"V Nguyen","year":"2019","unstructured":"Nguyen V, Hough R, Bernaudo S, et al. Wnt\/beta-catenin signalling in ovarian cancer: insights into its hyperactivation and function in tumorigenesis. J Ovarian Res. 2019;12:122. https:\/\/doi.org\/10.1186\/s13048-019-0596-z.","journal-title":"J Ovarian Res"},{"issue":"9","key":"6143_CR66","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.3390\/cancers16091781","volume":"16","author":"K Balakrishnan","year":"2024","unstructured":"Balakrishnan K, Chen Y, Dong J. Amplification of hippo signaling pathway genes is governed and implicated in the serous subtype-specific ovarian carcino-genesis. Cancers (Basel). 2024;16(9):1781. https:\/\/doi.org\/10.3390\/cancers16091781.","journal-title":"Cancers (Basel)"},{"key":"6143_CR67","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/s41580-021-00404-3","volume":"23","author":"HK Matthews","year":"2022","unstructured":"Matthews HK, Bertoli C, de Bruin R. Cell cycle control in cancer. Nat Rev Mol Cell Biol. 2022;23:74\u201388. https:\/\/doi.org\/10.1038\/s41580-021-00404-3.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"6143_CR68","doi-asserted-by":"publisher","unstructured":"Rao Z, Ding Y. Ubiquitin pathway and ovarian cancer Curr Oncol. 2012;19(6):324\u20138. https:\/\/doi.org\/10.3747\/co.19.1175. Erratum. In: Curr Oncol. 2013;20(3):e280.","DOI":"10.3747\/co.19.1175"},{"issue":"6","key":"6143_CR69","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.1093\/bib\/bbx066","volume":"19","author":"J Yan","year":"2018","unstructured":"Yan J, Risacher SL, Shen L, Saykin AJ. Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. Brief Bioinform. 2018;19(6):1370\u201381. https:\/\/doi.org\/10.1093\/bib\/bbx066.","journal-title":"Brief Bioinform"},{"key":"6143_CR70","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.cancergen.2024.09.001","volume":"288\u2013289","author":"L Jahangiri","year":"2024","unstructured":"Jahangiri L. Updates on liquid biopsies in neuroblastoma for treatment response, relapse and recurrence assessment. Cancer Genet. 2024;288\u2013289:32\u20139. https:\/\/doi.org\/10.1016\/j.cancergen.2024.09.001.","journal-title":"Cancer Genet"},{"key":"6143_CR71","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/j.cancergen.2023.12.002","volume":"280\u2013281","author":"H Ohyama","year":"2024","unstructured":"Ohyama H, Hirotsu Y, Amemiya K, Mikata R, Amano H, Hirose S, et al. Development of a molecular barcode detection system for pancreaticobiliary malignancies and comparison with next-generation sequencing. Cancer Genet. 2024;280\u2013281:6\u201312. https:\/\/doi.org\/10.1016\/j.cancergen.2023.12.002.","journal-title":"Cancer Genet"},{"key":"6143_CR72","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cancergen.2023.12.003","volume":"282\u2013283","author":"T Gonzalez","year":"2024","unstructured":"Gonzalez T, Nie Q, Chaudhary LN, Basel D, Reddi HV, et al. Methylation signatures as biomarkers for non-invasive early detection of breast cancer: a systematic review of the literature. Cancer Genet. 2024;282\u2013283:1\u20138. https:\/\/doi.org\/10.1016\/j.cancergen.2023.12.003.","journal-title":"Cancer Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06143-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-025-06143-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06143-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T13:03:06Z","timestamp":1747141386000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-025-06143-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,13]]},"references-count":72,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["6143"],"URL":"https:\/\/doi.org\/10.1186\/s12859-025-06143-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.10.18.619017","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,13]]},"assertion":[{"value":"28 November 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 April 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"We confirm that all methods and procedures conducted in this study were carried out in accordance with the relevant guidelines and regulations set forth by The Cancer Genome Atlas in regards to human subjects protection and data access policies.","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 Interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"126"}}