{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T16:34:50Z","timestamp":1773160490335,"version":"3.50.1"},"reference-count":77,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2018,2,1]],"date-time":"2018-02-01T00:00:00Z","timestamp":1517443200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1123042"],"award-info":[{"award-number":["1123042"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>It is known that noncoding RNAs (ncRNAs) cover \u223c98% of the transcriptome, but do not encode proteins. Among ncRNAs, long noncoding RNAs (lncRNAs) are a large and diverse class of RNA molecules, and are thought to be a gold mine of potential oncogenes, anti-oncogenes and new biomarkers. Although only a minority of lncRNAs is functionally characterized, it is clear that they are important regulators to modulate gene expression and involve in many biological functions. To reveal the functions and regulatory mechanisms of lncRNAs, it is vital to understand how lncRNAs regulate their target genes for implementing specific biological functions. In this article, we review the computational methods for inferring lncRNA\u2013mRNA interactions and the third-party databases of storing lncRNA\u2013mRNA regulatory relationships. We have found that the existing methods are based on statistical correlations between the gene expression levels of lncRNAs and mRNAs, and may not reveal gene regulatory relationships which are causal relationships. Moreover, these methods do not consider the modularity of lncRNA\u2013mRNA regulatory networks, and thus, the networks identified are not module-specific. To address the above two issues, we propose a novel method, MSLCRN, to infer and analyze module-specific lncRNA\u2013mRNA causal regulatory networks. We have applied it into glioblastoma multiforme, lung squamous cell carcinoma, ovarian cancer and prostate cancer, respectively. The experimental results show that MSLCRN, as an expression-based method, could be a useful complementary method to study lncRNA regulations.<\/jats:p>","DOI":"10.1093\/bib\/bby008","type":"journal-article","created":{"date-parts":[[2018,1,16]],"date-time":"2018-01-16T15:09:53Z","timestamp":1516115393000},"page":"1403-1419","source":"Crossref","is-referenced-by-count":47,"title":["Inferring and analyzing module-specific lncRNA\u2013mRNA causal regulatory networks in human cancer"],"prefix":"10.1093","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6127-9701","authenticated-orcid":false,"given":"Junpeng","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thuc Duy","family":"Le","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuyong","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,2,1]]},"reference":[{"issue":"1","key":"2019100807485605400_bby008-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.tig.2005.10.003","article-title":"Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function","volume":"22","author":"Pang","year":"2006","journal-title":"Trends Genet"},{"issue":"3","key":"2019100807485605400_bby008-B2","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1534\/genetics.112.146704","article-title":"Long noncoding RNAs: past, present, and future","volume":"193","author":"Kung","year":"2013","journal-title":"Genetics"},{"issue":"4","key":"2019100807485605400_bby008-B3","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.ccell.2016.03.010","article-title":"Long noncoding RNAs in cancer pathways","volume":"29","author":"Schmitt","year":"2016","journal-title":"Cancer Cell"},{"key":"2019100807485605400_bby008-B4","article-title":"Long noncoding RNA: a crosslink in biological regulatory network","author":"Zhang","year":"2017","journal-title":"Brief Bioinform"},{"issue":"19","key":"2019100807485605400_bby008-B5","doi-asserted-by":"crossref","first-page":"3723","DOI":"10.1016\/j.jmb.2012.11.024","article-title":"Posttranscriptional gene regulation by long noncoding RNA","volume":"425","author":"Yoon","year":"2013","journal-title":"J Mol Biol"},{"issue":"6","key":"2019100807485605400_bby008-B6","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1093\/bioinformatics\/btk041","article-title":"GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing","volume":"22","author":"Gerlach","year":"2006","journal-title":"Bioinformatics"},{"issue":"10","key":"2019100807485605400_bby008-B7","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1093\/bioinformatics\/btl024","article-title":"Thermodynamics of RNA-RNA binding","volume":"22","author":"M\u00fcckstein","year":"2006","journal-title":"Bioinformatics"},{"issue":"22","key":"2019100807485605400_bby008-B8","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1093\/bioinformatics\/btn193","article-title":"RNAplex: a fast tool for RNA-RNA interaction search","volume":"24","author":"Tafer","year":"2008","journal-title":"Bioinformatics"},{"issue":"24","key":"2019100807485605400_bby008-B9","doi-asserted-by":"crossref","first-page":"2849","DOI":"10.1093\/bioinformatics\/btn544","article-title":"IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions","volume":"24","author":"Busch","year":"2008","journal-title":"Bioinformatics"},{"issue":"18","key":"2019100807485605400_bby008-B10","doi-asserted-by":"crossref","first-page":"i460","DOI":"10.1093\/bioinformatics\/btq372","article-title":"RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming","volume":"26","author":"Kato","year":"2010","journal-title":"Bioinformatics"},{"issue":"5","key":"2019100807485605400_bby008-B11","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1093\/bib\/bbu048","article-title":"LncTar: a tool for predicting the RNA targets of long noncoding RNAs","volume":"16","author":"Li","year":"2015","journal-title":"Brief Bioinform"},{"issue":"17","key":"2019100807485605400_bby008-B12","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/btx287","article-title":"RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach","volume":"33","author":"Fukunaga","year":"2017","journal-title":"Bioinformatics"},{"issue":"9","key":"2019100807485605400_bby008-B13","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1101\/gr.132159.111","article-title":"The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression","volume":"22","author":"Derrien","year":"2012","journal-title":"Genome Res"},{"issue":"1","key":"2019100807485605400_bby008-B14","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.bbagrm.2015.08.005","article-title":"The specificity of long noncoding RNA expression","volume":"1859","author":"Gloss","year":"2016","journal-title":"Biochim Biophys Acta"},{"key":"2019100807485605400_bby008-B15","first-page":"156","article-title":"Non-coding RNAs: a dynamic and complex network of gene regulation","volume":"7","author":"Munshi","year":"2016","journal-title":"J Pharmacogenomics Pharmacoproteomics"},{"issue":"9","key":"2019100807485605400_bby008-B16","doi-asserted-by":"crossref","first-page":"3864","DOI":"10.1093\/nar\/gkq1348","article-title":"Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network","volume":"39","author":"Liao","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2019100807485605400_bby008-B17","doi-asserted-by":"crossref","first-page":"17683","DOI":"10.1038\/srep17683","article-title":"Comprehensive analysis of lncRNA-mRNA co-expression patterns identifies immune-associated lncRNA biomarkers in ovarian cancer malignant progression","volume":"5","author":"Guo","year":"2015","journal-title":"Sci Rep"},{"issue":"10","key":"2019100807485605400_bby008-B18","doi-asserted-by":"crossref","first-page":"2107","DOI":"10.1039\/C7MB00375G","article-title":"Comprehensive analysis of long noncoding RNA-mRNA co-expression patterns in thyroid cancer","volume":"13","author":"Du","year":"2017","journal-title":"Mol Biosyst"},{"key":"2019100807485605400_bby008-B19","doi-asserted-by":"crossref","first-page":"32731","DOI":"10.1038\/srep32731","article-title":"Tissue-specific co-expression of long non-coding and coding RNAs associated with breast Cancer","volume":"6","author":"Wu","year":"2016","journal-title":"Sci Rep"},{"issue":"2","key":"2019100807485605400_bby008-B20","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell's functional organization","volume":"5","author":"Barab\u00e1si","year":"2004","journal-title":"Nat Rev Genet"},{"key":"2019100807485605400_bby008-B21","doi-asserted-by":"crossref","first-page":"559.","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"6A","key":"2019100807485605400_bby008-B22","doi-asserted-by":"crossref","first-page":"3133","DOI":"10.1214\/09-AOS685","article-title":"Estimating high-dimensional intervention effects from observational data","volume":"37","author":"Maathuis","year":"2009","journal-title":"Ann Stat"},{"issue":"4","key":"2019100807485605400_bby008-B23","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1038\/nmeth0410-247","article-title":"Predicting causal effects in large-scale systems from observational data","volume":"7","author":"Maathuis","year":"2010","journal-title":"Nat Methods"},{"key":"2019100807485605400_bby008-B24","article-title":"A fast PC algorithm for high dimensional causal discovery with multi-core PCs","author":"Le","year":"2016","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"7","key":"2019100807485605400_bby008-B25","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/nsmb.2591","article-title":"Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer","volume":"20","author":"Du","year":"2013","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"2019100807485605400_bby008-B26","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1748-7188-1-3","article-title":"Partition function and base pairing probabilities of RNA heterodimers","volume":"1","author":"Bernhart","year":"2006","journal-title":"Algorithms Mol Biol"},{"issue":"2","key":"2019100807485605400_bby008-B27","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1089\/cmb.2006.13.267","article-title":"RNA-RNA interaction prediction and antisense RNA target search","volume":"13","author":"Alkan","year":"2006","journal-title":"J Comput Biol"},{"issue":"2","key":"2019100807485605400_bby008-B28","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/bioinformatics\/btq634","article-title":"PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences","volume":"27","author":"Seemann","year":"2011","journal-title":"Bioinformatics"},{"issue":"21","key":"2019100807485605400_bby008-B29","doi-asserted-by":"crossref","first-page":"2738","DOI":"10.1093\/bioinformatics\/bts519","article-title":"RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model","volume":"28","author":"Wenzel","year":"2012","journal-title":"Bioinformatics"},{"key":"2019100807485605400_bby008-B30","first-page":"e60","article-title":"RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets","volume":"45","author":"Alkan","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2019100807485605400_bby008-B31","doi-asserted-by":"crossref","first-page":"1650016.","DOI":"10.1142\/S0219720016500165","article-title":"lncRNATargets: a platform for lncRNA target prediction based on nucleic acid thermodynamics","volume":"14","author":"Hu","year":"2016","journal-title":"J Bioinform Comput Biol"},{"key":"2019100807485605400_bby008-B32","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s12864-015-2307-5","article-title":"Comprehensive prediction of lncRNA-RNA interactions in human transcriptome","volume":"17(Suppl 1)","author":"Terai","year":"2016","journal-title":"BMC Genomics"},{"key":"2019100807485605400_bby008-B33","first-page":"1885","article-title":"LncRNA expression profiles reveal the co-expression network in human colorectal carcinoma","volume":"9","author":"Liu","year":"2016","journal-title":"Int J Clin Exp Pathol"},{"key":"2019100807485605400_bby008-B34","doi-asserted-by":"crossref","first-page":"3394","DOI":"10.12659\/MSM.900783","article-title":"Identification of potential key long non-coding RNAs and target genes associated with pneumonia using long non-coding RNA sequencing (lncRNA-Seq): a preliminary study","volume":"22","author":"Huang","year":"2016","journal-title":"Med Sci Monit"},{"issue":"3","key":"2019100807485605400_bby008-B35","doi-asserted-by":"crossref","first-page":"2045","DOI":"10.3892\/mmr.2016.5480","article-title":"Dynamic co-expression network analysis of lncRNAs and mRNAs associated with venous congestion","volume":"14","author":"Li","year":"2016","journal-title":"Mol Med Rep"},{"issue":"3","key":"2019100807485605400_bby008-B36","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.joca.2014.12.001","article-title":"Expression profile of long noncoding RNAs in cartilage from knee osteoarthritis patients","volume":"23","author":"Fu","year":"2015","journal-title":"Osteoarthritis Cartilage"},{"issue":"4","key":"2019100807485605400_bby008-B37","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1111\/cns.12498","article-title":"Expression profile of long noncoding RNAs in peripheral blood mononuclear cells from multiple sclerosis patients","volume":"22","author":"Zhang","year":"2016","journal-title":"CNS Neurosci Ther"},{"issue":"1","key":"2019100807485605400_bby008-B38","doi-asserted-by":"crossref","first-page":"15.","DOI":"10.1186\/s13062-017-0183-4","article-title":"Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome","volume":"12","author":"Iwakiri","year":"2017","journal-title":"Biol Direct"},{"key":"2019100807485605400_bby008-B39","first-page":"688","article-title":"Integrated mRNA and lncRNA expression profiling for exploring metastatic biomarkers of human intrahepatic cholangiocarcinoma","volume":"7","author":"Lv","year":"2017","journal-title":"Am J Cancer Res"},{"key":"2019100807485605400_bby008-B40","doi-asserted-by":"crossref","first-page":"baw057.","DOI":"10.1093\/database\/baw057","article-title":"NPInter v3.0: an upgraded database of noncoding RNA-associated interactions","volume":"2016","author":"Hao","year":"2016","journal-title":"Database"},{"key":"2019100807485605400_bby008-B41","doi-asserted-by":"crossref","first-page":"D983","DOI":"10.1093\/nar\/gks1099","article-title":"LncRNADisease: a database for long-non-coding RNA-associated diseases","volume":"41","author":"Chen","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2019100807485605400_bby008-B42","doi-asserted-by":"crossref","first-page":"D193","DOI":"10.1093\/nar\/gku1173","article-title":"LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression","volume":"43","author":"Jiang","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807485605400_bby008-B43","doi-asserted-by":"crossref","first-page":"bav083","DOI":"10.1093\/database\/bav083","article-title":"LncReg: a reference resource for lncRNA-associated regulatory networks","volume":"2015","author":"Zhou","year":"2015","journal-title":"Database"},{"key":"2019100807485605400_bby008-B44","doi-asserted-by":"crossref","first-page":"baw138","DOI":"10.1093\/database\/baw138","article-title":"IRNdb: the database of immunologically relevant non-coding RNAs","volume":"2016","author":"Denisenko","year":"2016","journal-title":"Database"},{"issue":"5","key":"2019100807485605400_bby008-B45","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.jgg.2017.01.004","article-title":"lncRInter: a database of experimentally validated long non-coding RNA interaction","volume":"44","author":"Liu","year":"2017","journal-title":"J Genet Genomics"},{"issue":"D1","key":"2019100807485605400_bby008-B46","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"2019100807485605400_bby008-B47","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1093\/bioinformatics\/btw017","article-title":"lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes","volume":"32","author":"Liu","year":"2016","journal-title":"Bioinformatics"},{"issue":"1","key":"2019100807485605400_bby008-B48","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1186\/s12859-016-1251-y","article-title":"BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori","volume":"17","author":"Zhou","year":"2016","journal-title":"BMC Bioinformatics"},{"issue":"17","key":"2019100807485605400_bby008-B49","doi-asserted-by":"crossref","first-page":"2480","DOI":"10.1093\/bioinformatics\/btu325","article-title":"lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs","volume":"30","author":"Park","year":"2014","journal-title":"Bioinformatics"},{"key":"2019100807485605400_bby008-B50","doi-asserted-by":"crossref","first-page":"bat034","DOI":"10.1093\/database\/bat034","article-title":"lncRNome: a comprehensive knowledgebase of human long noncoding RNAs","volume":"2013","author":"Bhartiya","year":"2013","journal-title":"Database"},{"key":"2019100807485605400_bby008-B51","doi-asserted-by":"crossref","first-page":"bav082","DOI":"10.1093\/database\/bav082","article-title":"Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data","volume":"2015","author":"Zhao","year":"2015","journal-title":"Database"},{"issue":"Suppl 3","key":"2019100807485605400_bby008-B52","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2164-16-S3-S2","article-title":"LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data","volume":"16","author":"Jiang","year":"2015","journal-title":"BMC Genomics"},{"key":"2019100807485605400_bby008-B53","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.compbiolchem.2014.01.003","article-title":"lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome","volume":"50","author":"Chan","year":"2014","journal-title":"Comput Biol Chem"},{"key":"2019100807485605400_bby008-B54","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v046.i11","article-title":"Fast R functions for robust correlations and hierarchical clustering","volume":"46","author":"Langfelder","year":"2012","journal-title":"J Stat Softw"},{"key":"2019100807485605400_bby008-B55","volume-title":"Causality: Models, Reasoning, and Inference","author":"Judea","year":"2000"},{"key":"2019100807485605400_bby008-B56","volume-title":"Causation, Prediction, and Search","author":"Spirtes","year":"2000","edition":"2nd edn."},{"key":"2019100807485605400_bby008-B57","article-title":"ParallelPC: an R package for efficient constraint based causal exploration","author":"Le","year":"2015","journal-title":"arXiv prepring"},{"issue":"4","key":"2019100807485605400_bby008-B58","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/molbev\/msi072","article-title":"Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks","volume":"22","author":"Hahn","year":"2005","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2019100807485605400_bby008-B59","doi-asserted-by":"crossref","first-page":"e1002910.","DOI":"10.1371\/journal.pcbi.1002910","article-title":"From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization","volume":"9","author":"Song","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2019100807485605400_bby008-B60","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3294-8","volume-title":"Modeling Survival Data: Extending the Cox Model","author":"Therneau","year":"2000"},{"issue":"5","key":"2019100807485605400_bby008-B61","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"issue":"1","key":"2019100807485605400_bby008-B62","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"issue":"1","key":"2019100807485605400_bby008-B63","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2019100807485605400_bby008-B64","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkv1094","article-title":"Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers","volume":"44","author":"Ning","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019100807485605400_bby008-B65","doi-asserted-by":"crossref","first-page":"e765.","DOI":"10.1038\/cddis.2013.292","article-title":"Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network","volume":"4","author":"Wang","year":"2013","journal-title":"Cell Death Dis"},{"issue":"D1","key":"2019100807485605400_bby008-B66","doi-asserted-by":"crossref","first-page":"D833","DOI":"10.1093\/nar\/gkw943","article-title":"DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants","volume":"45","author":"Pi\u00f1ero","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"2019100807485605400_bby008-B67","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"issue":"6","key":"2019100807485605400_bby008-B68","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/nrd4018","article-title":"Targeting long non-coding RNA to therapeutically upregulate gene expression","volume":"12","author":"Wahlestedt","year":"2013","journal-title":"Nat Rev Drug Discov"},{"key":"2019100807485605400_bby008-B69","first-page":"45","article-title":"Cytokine activity in cancer-related anorexia\/cachexia: role of megestrol acetate and medroxyprogesterone acetate","volume":"25","author":"Mantovani","year":"1998","journal-title":"Semin Oncol"},{"issue":"2","key":"2019100807485605400_bby008-B70","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/nrc2069","article-title":"G-protein-coupled receptors and cancer","volume":"7","author":"Dorsam","year":"2007","journal-title":"Nat Rev Cancer"},{"issue":"11","key":"2019100807485605400_bby008-B71","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1111\/j.1745-7254.2008.00889.x","article-title":"Tumor necrosis factor and cancer, buddies or foes?","volume":"29","author":"Wang","year":"2008","journal-title":"Acta Pharmacol Sin"},{"issue":"1","key":"2019100807485605400_bby008-B72","doi-asserted-by":"crossref","first-page":"436","DOI":"10.3390\/cancers6010436","article-title":"The role of cyclic nucleotide signaling pathways in cancer: targets for prevention and treatment","volume":"6","author":"Fajardo","year":"2014","journal-title":"Cancers"},{"issue":"5","key":"2019100807485605400_bby008-B73","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"issue":"1","key":"2019100807485605400_bby008-B74","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1093\/bioinformatics\/btr626","article-title":"Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information","volume":"28","author":"Zhang","year":"2012","journal-title":"Bioinformatics"},{"issue":"18","key":"2019100807485605400_bby008-B75","doi-asserted-by":"crossref","first-page":"5130","DOI":"10.1073\/pnas.1522586113","article-title":"Part mutual information for quantifying direct associations in networks","volume":"113","author":"Zhao","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"2019100807485605400_bby008-B76","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.1093\/nar\/gku1315","article-title":"Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks","volume":"43","author":"Zhang","year":"2015","journal-title":"Nucleic Acids Re"},{"issue":"4","key":"2019100807485605400_bby008-B77","first-page":"577","article-title":"Computational methods for identifying miRNA sponge interactions","volume":"18","author":"Le","year":"2017","journal-title":"Brief Bioinform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/20\/4\/1403\/30119494\/bby008.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/20\/4\/1403\/30119494\/bby008.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T07:52:51Z","timestamp":1570521171000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/20\/4\/1403\/4833470"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,2,1]]},"references-count":77,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2018,2,1]]},"published-print":{"date-parts":[[2019,7,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bby008","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7]]},"published":{"date-parts":[[2018,2,1]]}}}