{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T10:45:59Z","timestamp":1770461159918,"version":"3.49.0"},"reference-count":76,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,6,16]],"date-time":"2021-06-16T00:00:00Z","timestamp":1623801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,6,16]],"date-time":"2021-06-16T00:00:00Z","timestamp":1623801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>LncRNAs (Long non-coding RNAs) are a type of non-coding RNA molecule with transcript length longer than 200 nucleotides. LncRNA has been novel candidate biomarkers in cancer diagnosis and prognosis. However, it is difficult to discover the true association mechanism between lncRNAs and complex diseases. The unprecedented enrichment of multi-omics data and the rapid development of machine learning technology provide us with the opportunity to design a machine learning framework to study the relationship between lncRNAs and complex diseases.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this article, we proposed a new machine learning approach, namely LGDLDA (LncRNA-Gene-Disease association networks based LncRNA-Disease Association prediction), for disease-related lncRNAs association prediction based multi-omics data, machine learning methods and neural network neighborhood information aggregation. Firstly, LGDLDA calculates the similarity matrix of lncRNA, gene and disease respectively, and it calculates the similarity between lncRNAs through the lncRNA expression profile matrix, lncRNA-miRNA interaction matrix and lncRNA-protein interaction matrix. We obtain gene similarity matrix by calculating the lncRNA-gene association matrix and the gene-disease association matrix, and we obtain disease similarity matrix by calculating the disease ontology, the disease-miRNA association matrix, and Gaussian interaction profile kernel similarity. Secondly, LGDLDA integrates the neighborhood information in similarity matrices by using nonlinear feature learning of neural network. Thirdly, LGDLDA uses embedded node representations to approximate the observed matrices. Finally, LGDLDA ranks candidate lncRNA-disease pairs and then selects potential disease-related lncRNAs.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Compared with lncRNA-disease prediction methods, our proposed method takes into account more critical information and obtains the performance improvement cancer-related lncRNA predictions. Randomly split data experiment results show that the stability of LGDLDA is better than IDHI-MIRW, NCPLDA, LncDisAP and NCPHLDA. The results on different simulation data sets show that LGDLDA can accurately and effectively predict the disease-related lncRNAs. Furthermore, we applied the method to three real cancer data including gastric cancer, colorectal cancer and breast cancer to predict potential cancer-related lncRNAs.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04256-8","type":"journal-article","created":{"date-parts":[[2021,6,16]],"date-time":"2021-06-16T14:02:54Z","timestamp":1623852174000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":46,"title":["A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs"],"prefix":"10.1186","volume":"22","author":[{"given":"Lin","family":"Yuan","sequence":"first","affiliation":[]},{"given":"Jing","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Tao","family":"Sun","sequence":"additional","affiliation":[]},{"given":"Zhen","family":"Shen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,6,16]]},"reference":[{"issue":"1","key":"4256_CR1","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/nrg.2015.10","volume":"17","author":"JJ Quinn","year":"2016","unstructured":"Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet . 2016;17(1):47.","journal-title":"Nat Rev Genet"},{"key":"4256_CR2","first-page":"1","volume":"2017","author":"J Jarroux","year":"2017","unstructured":"Jarroux J, Morillon A, Pinskaya M. History, discovery, and classification of lncRNAs. Long Non Coding RNA Biol. 2017;2017:1\u201346.","journal-title":"Long Non Coding RNA Biol"},{"issue":"3","key":"4256_CR3","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/j.cell.2018.01.011","volume":"172","author":"F Kopp","year":"2018","unstructured":"Kopp F, Mendell JT. Functional classification and experimental dissection of long noncoding RNAs. Cell. 2018;172(3):393\u2013407.","journal-title":"Cell"},{"issue":"11","key":"4256_CR4","doi-asserted-by":"publisher","first-page":"440","DOI":"10.3390\/cancers10110440","volume":"10","author":"B Neve","year":"2018","unstructured":"Neve B, Jonckheere N, Vincent A, Van Seuningen I. Epigenetic regulation by lncRNAs: an overview focused on UCA1 in colorectal cancer. Cancers. 2018;10(11):440.","journal-title":"Cancers"},{"issue":"9","key":"4256_CR5","doi-asserted-by":"publisher","first-page":"eaao2110","DOI":"10.1126\/sciadv.aao2110","volume":"3","author":"Y Long","year":"2017","unstructured":"Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? Science Adv. 2017;3(9):eaao2110.","journal-title":"Science Adv"},{"issue":"1","key":"4256_CR6","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/j.gendis.2019.01.003","volume":"6","author":"R-Z He","year":"2019","unstructured":"He R-Z, Luo D-X, Mo Y-Y. Emerging roles of lncRNAs in the post-transcriptional regulation in cancer. Genes Dis. 2019;6(1):6.","journal-title":"Genes Dis"},{"key":"4256_CR7","unstructured":"C.-H. Zheng, L. Yuan, W. Sha, Z.-L. Sun, Gene differential coexpression analysis based on biweight correlation and maximum clique. p. S3."},{"issue":"10","key":"4256_CR8","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.2174\/1389450118666170622091940","volume":"19","author":"G Botti","year":"2018","unstructured":"Botti G, Collina F, Scognamiglio G, Aquino G, Cerrone M, Liguori G, Gigantino V, Malzone MG, Cantile M. LncRNA HOTAIR polymorphisms association with cancer susceptibility in different tumor types. Curr Drug Targets. 2018;19(10):1220\u20136.","journal-title":"Curr Drug Targets"},{"issue":"41","key":"4256_CR9","doi-asserted-by":"publisher","first-page":"5661","DOI":"10.1038\/onc.2017.184","volume":"36","author":"W-X Peng","year":"2017","unstructured":"Peng W-X, Koirala P, Mo Y-Y. LncRNA-mediated regulation of cell signaling in cancer. Oncogene. 2017;36(41):5661\u20137.","journal-title":"Oncogene"},{"key":"4256_CR10","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.vph.2018.01.003","volume":"114","author":"V Simion","year":"2019","unstructured":"Simion V, Haemmig S, Feinberg MW. LncRNAs in vascular biology and disease. Vascul Pharmacol. 2019;114:145\u201356.","journal-title":"Vascul Pharmacol"},{"issue":"3","key":"4256_CR11","doi-asserted-by":"publisher","first-page":"292","DOI":"10.2174\/1574892813666180226121819","volume":"13","author":"Y Zhang","year":"2018","unstructured":"Zhang Y, Tang L. The application of lncRNAs in cancer treatment and diagnosis. Recent Pat Anti-Cancer Drug Discovery. 2018;13(3):292\u2013301.","journal-title":"Recent Pat Anti-Cancer Drug Discovery"},{"issue":"D1","key":"4256_CR12","doi-asserted-by":"publisher","first-page":"D983","DOI":"10.1093\/nar\/gks1099","volume":"41","author":"G Chen","year":"2012","unstructured":"Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G, Cui Q. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 2012;41(D1):D983\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4256_CR13","doi-asserted-by":"publisher","first-page":"D980","DOI":"10.1093\/nar\/gkv1094","volume":"44","author":"S Ning","year":"2016","unstructured":"Ning S, Zhang J, Wang P, Zhi H, Wang J, Liu Y, Gao Y, Guo M, Yue M, Wang L. Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers. Nucleic Acids Res. 2016;44(D1):D980\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4256_CR14","doi-asserted-by":"publisher","first-page":"D203","DOI":"10.1093\/nar\/gkv1252","volume":"44","author":"Y Zhao","year":"2016","unstructured":"Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang MQ. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res. 2016;44(D1):D203\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"suppl_1","key":"4256_CR15","doi-asserted-by":"publisher","first-page":"D146","DOI":"10.1093\/nar\/gkq1138","volume":"39","author":"PP Amaral","year":"2011","unstructured":"Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 2011;39(suppl_1):D146\u201351.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4256_CR16","doi-asserted-by":"publisher","first-page":"D246","DOI":"10.1093\/nar\/gks915","volume":"41","author":"P-J Volders","year":"2013","unstructured":"Volders P-J, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P. LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res. 2013;41(D1):D246\u201351.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"4256_CR17","doi-asserted-by":"publisher","first-page":"3478","DOI":"10.1093\/nar\/gkv233","volume":"43","author":"P Wang","year":"2015","unstructured":"Wang P, Ning S, Zhang Y, Li R, Ye J, Zhao Z, Zhi H, Wang T, Guo Z, Li X. Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res. 2015;43(7):3478\u201389.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"4256_CR18","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/j.tig.2016.08.004","volume":"32","author":"B Signal","year":"2016","unstructured":"Signal B, Gloss BS, Dinger ME. Computational approaches for functional prediction and characterisation of long noncoding RNAs. Trends Genet. 2016;32(10):620\u201337.","journal-title":"Trends Genet"},{"issue":"17","key":"4256_CR19","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1186\/s12859-016-1332-y","volume":"17","author":"P-J Wei","year":"2016","unstructured":"Wei P-J, Zhang D, Xia J, Zheng C-H. LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network. BMC Bioinformatics. 2016;17(17):467.","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"4256_CR20","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1093\/bib\/bbx130","volume":"20","author":"X Chen","year":"2019","unstructured":"Chen X, Xie D, Zhao Q, You Z-H. MicroRNAs and complex diseases: from experimental results to computational models. Brief Bioinform. 2019;20(2):515\u201339.","journal-title":"Brief Bioinform"},{"issue":"8","key":"4256_CR21","doi-asserted-by":"publisher","first-page":"2074","DOI":"10.1039\/C3MB70608G","volume":"10","author":"J Sun","year":"2014","unstructured":"Sun J, Shi H, Wang Z, Zhang C, Liu L, Wang L, He W, Hao D, Liu S, Zhou M. Inferring novel lncRNA\u2013disease associations based on a random walk model of a lncRNA functional similarity network. Mol BioSyst. 2014;10(8):2074\u201381.","journal-title":"Mol BioSyst"},{"issue":"3","key":"4256_CR22","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1039\/C4MB00511B","volume":"11","author":"M Zhou","year":"2015","unstructured":"Zhou M, Wang X, Li J, Hao D, Wang Z, Shi H, Han L, Zhou H, Sun J. Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network. Mol BioSyst. 2015;11(3):760\u20139.","journal-title":"Mol BioSyst"},{"issue":"2","key":"4256_CR23","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1109\/TCBB.2017.2701379","volume":"16","author":"J Zhang","year":"2017","unstructured":"Zhang J, Zhang Z, Chen Z, Deng L. Integrating multiple heterogeneous networks for novel lncRNA-disease association inference. IEEE\/ACM Trans Comput Biol Bioinf. 2017;16(2):396\u2013406.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"key":"4256_CR24","doi-asserted-by":"publisher","first-page":"39516","DOI":"10.1038\/srep39516","volume":"7","author":"Q Yao","year":"2017","unstructured":"Yao Q, Wu L, Li J, L. guang Yang, Y. Sun, Z. Li, S. He, F. Feng, H. Li, and Y. Li, . Global prioritizing disease candidate lncRNAs via a multi-level composite network. Sci Rep. 2017;7:39516.","journal-title":"Sci Rep"},{"issue":"2","key":"4256_CR25","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1109\/TNB.2015.2391133","volume":"14","author":"GU Ganegoda","year":"2015","unstructured":"Ganegoda GU, Li M, Wang W, Feng Q. Heterogeneous network model to infer human disease-long intergenic non-coding RNA associations. IEEE Trans Nanobiosci. 2015;14(2):175\u201383.","journal-title":"IEEE Trans Nanobiosci"},{"issue":"19","key":"4256_CR26","doi-asserted-by":"publisher","first-page":"3357","DOI":"10.1093\/bioinformatics\/bty327","volume":"34","author":"C Lu","year":"2018","unstructured":"Lu C, Yang M, Luo F, Wu F-X, Li M, Pan Y, Li Y, Wang J. Prediction of lncRNA\u2013disease associations based on inductive matrix completion. Bioinformatics. 2018;34(19):3357\u201364.","journal-title":"Bioinformatics"},{"issue":"20","key":"4256_CR27","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1093\/bioinformatics\/btt426","volume":"29","author":"X Chen","year":"2013","unstructured":"Chen X, Yan G-Y. Novel human lncRNA\u2013disease association inference based on lncRNA expression profiles. Bioinformatics. 2013;29(20):2617\u201324.","journal-title":"Bioinformatics"},{"issue":"3","key":"4256_CR28","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1093\/bioinformatics\/btw639","volume":"33","author":"W Lan","year":"2017","unstructured":"Lan W, Li M, Zhao K, Liu J, Wu F-X, Pan Y, Wang J. LDAP: a web server for lncRNA-disease association prediction. Bioinformatics. 2017;33(3):458\u201360.","journal-title":"Bioinformatics"},{"key":"4256_CR29","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1016\/j.isci.2019.08.030","volume":"19","author":"Z-H Guo","year":"2019","unstructured":"Guo Z-H, You Z-H, Wang Y-B, Yi H-C, Chen Z-H. A learning-based method for LncRNA-disease association identification combing similarity information and rotation forest. iScience. 2019;19:786\u201395.","journal-title":"iScience"},{"issue":"7629","key":"4256_CR30","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1038\/nature20149","volume":"539","author":"JM Engreitz","year":"2016","unstructured":"Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature. 2016;539(7629):452\u20135.","journal-title":"Nature"},{"issue":"7341","key":"4256_CR31","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/nature09819","volume":"472","author":"KC Wang","year":"2011","unstructured":"Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011;472(7341):120\u20134.","journal-title":"Nature"},{"issue":"1","key":"4256_CR32","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.cell.2010.09.001","volume":"143","author":"UA \u00d8rom","year":"2010","unstructured":"\u00d8rom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010;143(1):46\u201358.","journal-title":"Cell"},{"issue":"3","key":"4256_CR33","doi-asserted-by":"publisher","first-page":"269","DOI":"10.2174\/1574893613666180703105258","volume":"14","author":"L Wang","year":"2019","unstructured":"Wang L, Xuan Z, Zhou S, Kuang L, Pei T. A novel model for predicting LncRNA-disease associations based on the LncRNA-MiRNA-Disease interactive network. Curr Bioinform. 2019;14(3):269\u201378.","journal-title":"Curr Bioinform"},{"issue":"9","key":"4256_CR34","doi-asserted-by":"publisher","first-page":"830","DOI":"10.2174\/0929866525666180905104904","volume":"25","author":"Q Zhao","year":"2018","unstructured":"Zhao Q, Liang D, Hu H, Ren G, Liu H. RWLPAP: random walk for lncRNA-protein associations prediction. Protein Pept Lett. 2018;25(9):830\u20137.","journal-title":"Protein Pept Lett"},{"issue":"3","key":"4256_CR35","doi-asserted-by":"publisher","first-page":"1005455","DOI":"10.1371\/journal.pcbi.1005455","volume":"13","author":"Z-H You","year":"2017","unstructured":"You Z-H, Huang Z-A, Zhu Z, Yan G-Y, Li Z-W, Wen Z, Chen X. PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction. PLoS Comput Biol . 2017;13(3):1005455.","journal-title":"PLoS Comput Biol"},{"key":"4256_CR36","unstructured":"H. Chen, X. Wang, X. Zhang, X. Zeng, T. Song, A. Rodr\u00edguez-Pat\u00f3n, LncRNA-disease association prediction based on neighborhood information aggregation in neural network, pp. 175\u2013178."},{"issue":"1","key":"4256_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-019-42010-6","volume":"9","author":"L Yuan","year":"2019","unstructured":"Yuan L, Huang D-S. A network-guided association mapping approach from DNA methylation to disease. Sci Rep. 2019;9(1):1\u201316.","journal-title":"Sci Rep"},{"issue":"D1","key":"4256_CR38","doi-asserted-by":"publisher","first-page":"D1034","DOI":"10.1093\/nar\/gky905","volume":"47","author":"Z Bao","year":"2019","unstructured":"Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q, Dong D. LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res. 2019;47(D1):D1034\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4256_CR39","first-page":"D371","volume":"46","author":"T Cui","year":"2018","unstructured":"Cui T, Zhang L, Huang Y, Yi Y, Tan P, Zhao Y, Hu Y, Xu L, Li E, Wang D. MNDR v2. 0: an updated resource of ncRNA\u2013disease associations in mammals. Nucleic Acids Res. 2018;46(D1):D371\u20134.","journal-title":"Nucleic Acids Res"},{"key":"4256_CR40","doi-asserted-by":"publisher","first-page":"58849","DOI":"10.1109\/ACCESS.2019.2914533","volume":"7","author":"G Li","year":"2019","unstructured":"Li G, Luo J, Liang C, Xiao Q, Ding P, Zhang Y. Prediction of LncRNA-disease associations based on network consistency projection. IEEE Access. 2019;7:58849\u201356.","journal-title":"IEEE Access"},{"issue":"1","key":"4256_CR41","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/s12859-019-2675-y","volume":"20","author":"X-N Fan","year":"2019","unstructured":"Fan X-N, Zhang S-W, Zhang S-Y, Zhu K, Lu S. Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. BMC Bioinf. 2019;20(1):87.","journal-title":"BMC Bioinf"},{"issue":"16","key":"4256_CR42","first-page":"1","volume":"20","author":"Y Wang","year":"2019","unstructured":"Wang Y, Juan L, Peng J, Zang T, Wang Y. LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. BMC Bioinform. 2019;20(16):1\u201311.","journal-title":"BMC Bioinform"},{"key":"4256_CR43","doi-asserted-by":"crossref","unstructured":"Zhang H, Liang Y, Peng C, Han S, Du W, Li Y. Predicting lncRNA-disease associations using network topological similarity based on deep mining heterogeneous networks. Math Biosci. 2019;315.","DOI":"10.1016\/j.mbs.2019.108229"},{"issue":"6","key":"4256_CR44","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/s12920-018-0430-2","volume":"11","author":"J Wang","year":"2018","unstructured":"Wang J, Zhang X, Chen W, Li J, Liu C. CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features. BMC Med Genom. 2018;11(6):114.","journal-title":"BMC Med Genom"},{"issue":"D1","key":"4256_CR45","doi-asserted-by":"publisher","first-page":"D187","DOI":"10.1093\/nar\/gku1167","volume":"43","author":"L Ma","year":"2015","unstructured":"Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res. 2015;43(D1):D187\u201392.","journal-title":"Nucleic Acids Res"},{"issue":"7418","key":"4256_CR46","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/nature11412","volume":"490","author":"CGA Network","year":"2012","unstructured":"Network CGA. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61.","journal-title":"Nature"},{"key":"4256_CR47","doi-asserted-by":"crossref","unstructured":"L. Yuan, C.-H. Zheng, J.-F. Xia, D.-S. Huang, Module based differential coexpression analysis method for type 2 diabetes. BioMed Res Int, 2015, 2015.","DOI":"10.1155\/2015\/836929"},{"issue":"2","key":"4256_CR48","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.canlet.2014.11.005","volume":"356","author":"X-Y Fang","year":"2015","unstructured":"Fang X-Y, Pan H-F, Leng R-X, Ye D-Q. Long noncoding RNAs: novel insights into gastric cancer. Cancer Lett. 2015;356(2):357\u201366.","journal-title":"Cancer Lett"},{"issue":"5","key":"4256_CR49","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1109\/TCBB.2016.2609420","volume":"14","author":"L Yuan","year":"2016","unstructured":"Yuan L, Zhu L, Guo W-L, Zhou X, Zhang Y, Huang Z, Huang D-S. Nonconvex penalty based low-rank representation and sparse regression for eQTL mapping. IEEE\/ACM Trans Comput Biol Bioinf. 2016;14(5):1154\u201364.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"issue":"6","key":"4256_CR50","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1007\/s00432-017-2361-2","volume":"143","author":"L Pan","year":"2017","unstructured":"Pan L, Liang W, Fu M, Huang Z-H, Li X, Zhang W, Zhang P, Qian H, Jiang P-C, Xu W-R. Exosomes-mediated transfer of long noncoding RNA ZFAS1 promotes gastric cancer progression. J Cancer Res Clin Oncol. 2017;143(6):991\u20131004.","journal-title":"J Cancer Res Clin Oncol"},{"key":"4256_CR51","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1042\/BSR20171070","volume":"37","author":"Z Mao","year":"2017","unstructured":"Mao Z, Li H, Du B, Cui K, Xing Y, Zhao X, Zai S. LncRNA DANCR promotes migration and invasion through suppression of lncRNA-LET in gastric cancer cells. Biosci Rep. 2017;37:6.","journal-title":"Biosci Rep"},{"issue":"21","key":"4256_CR52","doi-asserted-by":"publisher","first-page":"6299","DOI":"10.1158\/0008-5472.CAN-16-0356","volume":"76","author":"M Sun","year":"2016","unstructured":"Sun M, Nie F, Wang Y, Zhang Z, Hou J, He D, Xie M, Xu L, De W, Wang Z. LncRNA HOXA11-AS promotes proliferation and invasion of gastric cancer by scaffolding the chromatin modification factors PRC2, LSD1, and DNMT1. Can Res. 2016;76(21):6299\u2013310.","journal-title":"Can Res"},{"issue":"6","key":"4256_CR53","doi-asserted-by":"publisher","first-page":"303","DOI":"10.3390\/genes9060303","volume":"9","author":"H Liu","year":"2018","unstructured":"Liu H, Zhang Z, Wu N, Guo H, Zhang H, Fan D, Nie Y, Liu Y. Integrative analysis of dysregulated lncRNA-associated ceRNA network reveals functional lncRNAs in gastric cancer. Genes. 2018;9(6):303.","journal-title":"Genes"},{"key":"4256_CR54","doi-asserted-by":"crossref","unstructured":"V. G. Vogel, Epidemiology of breast cancer, The breast, 207\u2013218. e4. Elsevier, 2018.","DOI":"10.1016\/B978-0-323-35955-9.00015-5"},{"issue":"5","key":"4256_CR55","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1109\/TCBB.2016.2621769","volume":"14","author":"S-G Ge","year":"2016","unstructured":"Ge S-G, Xia J, Sha W, Zheng C-H. Cancer subtype discovery based on integrative model of multigenomic data. IEEE\/ACM Trans Comput Biol Bioinf. 2016;14(5):1115\u201321.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"key":"4256_CR56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12943-020-01206-5","volume":"19","author":"Y Liang","year":"2020","unstructured":"Liang Y, Song X, Li Y, Chen B, Zhao W, Wang L, Zhang H, Liu Y, Han D, Zhang N. LncRNA BCRT1 promotes breast cancer progression by targeting miR-1303\/PTBP3 axis. Mol Cancer. 2020;19:1\u201320.","journal-title":"Mol Cancer"},{"issue":"1","key":"4256_CR57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-017-12716-6","volume":"7","author":"AJ Gooding","year":"2017","unstructured":"Gooding AJ, Zhang B, Jahanbani FK, Gilmore HL, Chang JC, Valadkhan S, Schiemann WP. The lncRNA BORG drives breast cancer metastasis and disease recurrence. Sci Rep. 2017;7(1):1\u201318.","journal-title":"Sci Rep"},{"issue":"1","key":"4256_CR58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-020-20207-y","volume":"11","author":"K-C Chang","year":"2020","unstructured":"Chang K-C, Diermeier SD, Allen TY, Brine LD, Russo S, Bhatia S, Alsudani H, Kostroff K, Bhuiya T, Brogi E. MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression. Nat Commun. 2020;11(1):1\u201319.","journal-title":"Nat Commun"},{"issue":"2","key":"4256_CR59","doi-asserted-by":"publisher","first-page":"63","DOI":"10.14740\/wjon1191","volume":"10","author":"P Rawla","year":"2019","unstructured":"Rawla P. Epidemiology of prostate cancer. World J Oncol. 2019;10(2):63.","journal-title":"World J Oncol"},{"key":"4256_CR60","doi-asserted-by":"crossref","unstructured":"L. Yuan, C.-A. Yuan, D.-S. Huang, FAACOSE: A fast adaptive ant colony optimization algorithm for detecting SNP epistasis, Complexity, 2017, 2017.","DOI":"10.1155\/2017\/5024867"},{"issue":"3","key":"4256_CR61","doi-asserted-by":"publisher","first-page":"613","DOI":"10.3233\/CBM-170683","volume":"21","author":"B Zhao","year":"2018","unstructured":"Zhao B, Lu Y-L, Yang Y, Hu L-B, Bai Y, Li R-Q, Zhang G-Y, Li J, Bi C-W, Yang L-B. Overexpression of lncRNA ANRIL promoted the proliferation and migration of prostate cancer cells via regulating let-7a\/TGF-\u03b21\/Smad signaling pathway. Cancer Biomark. 2018;21(3):613\u201320.","journal-title":"Cancer Biomark"},{"issue":"1","key":"4256_CR62","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.bbrc.2017.03.169","volume":"487","author":"J Li","year":"2017","unstructured":"Li J, Zhang Z, Xiong L, Guo C, Jiang T, Zeng L, Li G, Wang J. SNHG1 lncRNA negatively regulates miR-199a-3p to enhance CDK7 expression and promote cell proliferation in prostate cancer. Biochem Biophys Res Commun. 2017;487(1):146\u201352.","journal-title":"Biochem Biophys Res Commun"},{"issue":"8","key":"4256_CR63","doi-asserted-by":"publisher","first-page":"e0182305","DOI":"10.1371\/journal.pone.0182305","volume":"12","author":"Y Zhang","year":"2017","unstructured":"Zhang Y, Su X, Kong Z, Fu F, Zhang P, Wang D, Wu H, Wan X, Li Y. An androgen reduced transcript of LncRNA GAS5 promoted prostate cancer proliferation. PLoS ONE. 2017;12(8):e0182305.","journal-title":"PLoS ONE"},{"issue":"D1","key":"4256_CR64","doi-asserted-by":"publisher","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","volume":"42","author":"J-H Li","year":"2014","unstructured":"Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H. starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein\u2013RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(D1):D92\u20137.","journal-title":"Nucleic Acids Res"},{"key":"4256_CR65","doi-asserted-by":"crossref","unstructured":"Y. Hao, W. Wu, H. Li, J. Yuan, J. Luo, Y. Zhao, R. Chen, NPInter v3. 0: an upgraded database of noncoding RNA-associated interactions, Database, 2016, 2016.","DOI":"10.1093\/database\/baw057"},{"issue":"D1","key":"4256_CR66","doi-asserted-by":"publisher","first-page":"D115","DOI":"10.1093\/nar\/gkw1052","volume":"45","author":"Y Yi","year":"2017","unstructured":"Yi Y, Zhao Y, Li C, Zhang L, Huang H, Li Y, Liu L, Hou P, Cui T, Tan P. RAID v2. 0: an updated resource of RNA-associated interactions across organisms. Nucleic Acids Res. 2017;45(D1):D115\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4256_CR67","doi-asserted-by":"publisher","first-page":"D1013","DOI":"10.1093\/nar\/gky1010","volume":"47","author":"Z Huang","year":"2019","unstructured":"Huang Z, Shi J, Gao Y, Cui C, Zhang S, Li J, Zhou Y, Cui Q. HMDD v3. 0: a database for experimentally supported human microRNA\u2013disease associations. Nucleic Acids Res. 2019;47(D1):D1013\u20137.","journal-title":"Nucleic Acids Res"},{"key":"4256_CR68","doi-asserted-by":"crossref","unstructured":"J. Pi\u00f1ero, \u00c0. Bravo, N. Queralt-Rosinach, A. Guti\u00e9rrez-Sacrist\u00e1n, J. Deu-Pons, E. Centeno, J. Garc\u00eda-Garc\u00eda, F. Sanz, L. I. Furlong, DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants, Nucleic acids research, gkw943, 2016.","DOI":"10.1093\/nar\/gkw943"},{"issue":"D1","key":"4256_CR69","doi-asserted-by":"publisher","first-page":"D121","DOI":"10.1093\/nar\/gky1144","volume":"47","author":"P Wang","year":"2019","unstructured":"Wang P, Li X, Gao Y, Guo Q, Wang Y, Fang Y, Ma X, Zhi H, Zhou D, Shen W. LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low-and high-throughput experiments. Nucleic Acids Res. 2019;47(D1):D121\u20137.","journal-title":"Nucleic Acids Res"},{"key":"4256_CR70","doi-asserted-by":"publisher","first-page":"11","DOI":"10.18637\/jss.v046.i11","volume":"46","author":"P Langfelder","year":"2012","unstructured":"Langfelder P, Horvath S. Fast R functions for robust correlations and hierarchical clustering. J Stat Softw. 2012;46:11.","journal-title":"J Stat Softw"},{"issue":"3","key":"4256_CR71","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1109\/TCBB.2018.2866836","volume":"16","author":"L Yuan","year":"2018","unstructured":"Yuan L, Guo L-H, Yuan C-A, Zhang Y, Han K, Nandi AK, Honig B, Huang D-S. Integration of multi-omics data for gene regulatory network inference and application to breast cancer. IEEE\/ACM Trans Comput Biol Bioinf. 2018;16(3):782\u201391.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"issue":"21","key":"4256_CR72","doi-asserted-by":"publisher","first-page":"3036","DOI":"10.1093\/bioinformatics\/btr500","volume":"27","author":"T van Laarhoven","year":"2011","unstructured":"van Laarhoven T, Nabuurs SB, Marchiori E. Gaussian interaction profile kernels for predicting drug\u2013target interaction. Bioinformatics. 2011;27(21):3036\u201343.","journal-title":"Bioinformatics"},{"issue":"4","key":"4256_CR73","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1093\/bioinformatics\/btu684","volume":"31","author":"G Yu","year":"2015","unstructured":"Yu G, Wang L-G, Yan G-R, He Q-Y. DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2015;31(4):608\u20139.","journal-title":"Bioinformatics"},{"issue":"1","key":"4256_CR74","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1186\/1471-2105-12-266","volume":"12","author":"J Li","year":"2011","unstructured":"Li J, Gong B, Chen X, Liu T, Wu C, Zhang F, Li C, Li X, Rao S, Li X. DOSim: an R package for similarity between diseases based on disease ontology. BMC Bioinform. 2011;12(1):266.","journal-title":"BMC Bioinform"},{"issue":"1","key":"4256_CR75","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-017-00680-8","volume":"8","author":"Y Luo","year":"2017","unstructured":"Luo Y, Zhao X, Zhou J, Yang J, Zhang Y, Kuang W, Peng J, Chen L, Zeng J. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. Nat Commun. 2017;8(1):1\u201313.","journal-title":"Nat Commun"},{"issue":"22","key":"4256_CR76","doi-asserted-by":"publisher","first-page":"3873","DOI":"10.1093\/bioinformatics\/bty440","volume":"34","author":"V Gligorijevi\u0107","year":"2018","unstructured":"Gligorijevi\u0107 V, Barot M, Bonneau R. deepNF: deep network fusion for protein function prediction. Bioinformatics. 2018;34(22):3873\u201381.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-021-04256-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-021-04256-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-021-04256-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,4]],"date-time":"2023-02-04T01:03:53Z","timestamp":1675472633000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-021-04256-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,16]]},"references-count":76,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,12]]}},"alternative-id":["4256"],"URL":"https:\/\/doi.org\/10.1186\/s12859-021-04256-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,16]]},"assertion":[{"value":"31 January 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 June 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2021","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":"332"}}