{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:16:05Z","timestamp":1773274565306,"version":"3.50.1"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in post-transcriptional regulations as well as other important biological processes. Recently, accumulating evidences indicate that miRNAs are extensively involved in cancer. However, it is a big challenge to identify which miRNAs are related to which cancer considering the complex processes involved in tumors, where one miRNA may target hundreds or even thousands of genes and one gene may regulate multiple miRNAs. Despite integrative analysis of matched gene and miRNA expression data can help identify cancer-associated miRNAs, such kind of data is not commonly available. On the other hand, there are huge amount of gene expression data that are publicly accessible. It will significantly improve the efficiency of characterizing miRNA\u2019s function in cancer if we can identify cancer miRNAs directly from gene expression data.<\/jats:p>\n               <jats:p>Results: We present a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles without requiring either miRNA expression data or the matched gene and miRNA expression data. The results on multiple cancer datasets show that our proposed method can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches. Furthermore, some of our novel predictions are validated by both differentially expressed miRNAs and evidences from literature, implying the predictive power of our proposed method. In addition, we construct a cancer-miRNA-pathway network, which can help explain how miRNAs are involved in cancer.<\/jats:p>\n               <jats:p>Availability and implementation: The R code and data files for the proposed method are available at http:\/\/comp-sysbio.org\/miR_Path\/<\/jats:p>\n               <jats:p>Contact: \u00a0liukeq@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu811","type":"journal-article","created":{"date-parts":[[2014,12,14]],"date-time":"2014-12-14T01:33:54Z","timestamp":1418520834000},"page":"1226-1234","source":"Crossref","is-referenced-by-count":74,"title":["Identifying cancer-related microRNAs based on gene expression data"],"prefix":"10.1093","volume":"31","author":[{"given":"Xing-Ming","family":"Zhao","sequence":"first","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke-Qin","family":"Liu","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guanghui","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"He","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B\u00e9atrice","family":"Duval","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Michel","family":"Richer","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"De-Shuang","family":"Huang","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang-Jun","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin-Kao","family":"Hao","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luonan","family":"Chen","sequence":"additional","affiliation":[{"name":"1 School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 2Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA, 3LERIA, University of Angers, 49045 Angers Cedex 01, France, 4Department of Mathematics, Shanghai University, Shanghai 200444, China and 5Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,12,12]]},"reference":[{"key":"2023051309020112200_btu811-B1","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/wrna.4","article-title":"Posttranscriptional regulation of cancer traits by HuR","volume":"1","author":"Abdelmohsen","year":"2010","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"2023051309020112200_btu811-B2","doi-asserted-by":"crossref","first-page":"6979","DOI":"10.1038\/sj.onc.1210508","article-title":"The transcription factor ZEB1 (deltaEF1) promotes tumour cell dedifferentiation by repressing master regulators of epithelial polarity","volume":"26","author":"Aigner","year":"2007","journal-title":"Oncogene"},{"key":"2023051309020112200_btu811-B3","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1248\/bpb.29.903","article-title":"let-7 microRNA functions as a potential growth suppressor in human colon cancer cells","volume":"29","author":"Akao","year":"2006","journal-title":"Biol. Pharm. Bull."},{"key":"2023051309020112200_btu811-B4","doi-asserted-by":"crossref","first-page":"2128","DOI":"10.1038\/sj.onc.1210856","article-title":"MicroRNA-21 (miR-21) post-transcriptionally downregulates tumor suppressor Pdcd4 and stimulates invasion, intravasation and metastasis in colorectal cancer","volume":"27","author":"Asangani","year":"2008","journal-title":"Oncogene"},{"key":"2023051309020112200_btu811-B5","doi-asserted-by":"crossref","first-page":"6609","DOI":"10.1158\/0008-5472.CAN-10-0622","article-title":"Epigenetic silencing of miR-137 is an early event in colorectal carcinogenesis","volume":"70","author":"Balaguer","year":"2010","journal-title":"Cancer Res."},{"key":"2023051309020112200_btu811-B6","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2023051309020112200_btu811-B7","doi-asserted-by":"crossref","first-page":"3976","DOI":"10.3748\/wjg.v17.i35.3976","article-title":"MicroRNAs as a potential prognostic factor in gastric cancer","volume":"17","author":"Brenner","year":"2011","journal-title":"World J. Gastroenterol."},{"key":"2023051309020112200_btu811-B8","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nrc1997","article-title":"MicroRNA signatures in human cancers","volume":"6","author":"Calin","year":"2006","journal-title":"Nat. Rev. Cancer"},{"key":"2023051309020112200_btu811-B9","doi-asserted-by":"crossref","first-page":"15524","DOI":"10.1073\/pnas.242606799","article-title":"Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia","volume":"99","author":"Calin","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023051309020112200_btu811-B10","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1056\/NEJMoa050995","article-title":"A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia","volume":"353","author":"Calin","year":"2005","journal-title":"N. Engl. J. Med."},{"key":"2023051309020112200_btu811-B11","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/carcin\/bgs400","article-title":"Overexpression of paxillin induced by miR-137 suppression promotes tumor progression and metastasis in colorectal cancer","volume":"34","author":"Chen","year":"2013","journal-title":"Carcinogenesis"},{"key":"2023051309020112200_btu811-B12","doi-asserted-by":"crossref","first-page":"2792","DOI":"10.1039\/c2mb25180a","article-title":"RWRMDA: predicting novel human microRNA\u2013disease associations","volume":"8","author":"Chen","year":"2012","journal-title":"Mol. Biosyst."},{"key":"2023051309020112200_btu811-B13","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1016\/S1097-2765(01)00260-X","article-title":"The two-handed E box binding zinc finger protein SIP1 downregulates E-cadherin and induces invasion","volume":"7","author":"Comijn","year":"2001","journal-title":"Mol. Cell"},{"key":"2023051309020112200_btu811-B14","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1038\/nrg2634","article-title":"Causes and consequences of microRNA dysregulation in cancer","volume":"10","author":"Croce","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023051309020112200_btu811-B15","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.ejca.2008.10.032","article-title":"Genome-wide expression profile of sporadic gastric cancers with microsatellite instability","volume":"45","author":"D'Errico","year":"2009","journal-title":"Eur. J. Cancer"},{"key":"2023051309020112200_btu811-B16","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/j.gene.2012.12.103","article-title":"MicroRNA-195 and microRNA-378 mediate tumor growth suppression by epigenetical regulation in gastric cancer","volume":"518","author":"Deng","year":"2013","journal-title":"Gene"},{"key":"2023051309020112200_btu811-B17","doi-asserted-by":"crossref","first-page":"e72662","DOI":"10.1371\/journal.pone.0072662","article-title":"miR-26a suppresses tumor growth and metastasis by targeting FGF9 in gastric cancer","volume":"8","author":"Deng","year":"2013","journal-title":"PLoS One"},{"key":"2023051309020112200_btu811-B18","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1172\/JCI12973","article-title":"Altered expression of the mRNA stability factor HuR promotes cyclooxygenase-2 expression in colon cancer cells","volume":"108","author":"Dixon","year":"2001","journal-title":"J. Clin. Invest."},{"key":"2023051309020112200_btu811-B19","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023051309020112200_btu811-B20","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/nrg3074","article-title":"Non-coding RNAs in human disease","volume":"12","author":"Esteller","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023051309020112200_btu811-B21","doi-asserted-by":"crossref","first-page":"15805","DOI":"10.1073\/pnas.0707628104","article-title":"MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B","volume":"104","author":"Fabbri","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023051309020112200_btu811-B64","first-page":"1284","article-title":"Gene expression in histologically normal epithelium from breast cancer patients and from cancer-free prophylactic mastectomy patients shares a similar profile","volume":"102","author":"Graham","year":"2010","journal-title":"Br J Cancer 2010"},{"key":"2023051309020112200_btu811-B22","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: microRNA sequences, targets and gene nomenclature","volume":"34","author":"Griffiths-Jones","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023051309020112200_btu811-B23","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"},{"key":"2023051309020112200_btu811-B24","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s10585-010-9305-4","article-title":"A \u2018metastasis-prone\u2019 signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics","volume":"27","author":"Hong","year":"2010","journal-title":"Clin. Exp. Metastasis"},{"key":"2023051309020112200_btu811-B25","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023051309020112200_btu811-B26","doi-asserted-by":"crossref","first-page":"e363","DOI":"10.1371\/journal.pbio.0020363","article-title":"Human MicroRNA targets","volume":"2","author":"John","year":"2004","journal-title":"PLoS Biol."},{"key":"2023051309020112200_btu811-B27","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cell.2005.01.014","article-title":"RAS is regulated by the let-7 microRNA family","volume":"120","author":"Johnson","year":"2005","journal-title":"Cell"},{"key":"2023051309020112200_btu811-B28","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"Kanehisa","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023051309020112200_btu811-B29","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nrc2389","article-title":"Wnt signalling and its impact on development and cancer","volume":"8","author":"Klaus","year":"2008","journal-title":"Nat. Rev. Cancer"},{"key":"2023051309020112200_btu811-B30","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/ng1536","article-title":"Combinatorial microRNA target predictions","volume":"37","author":"Krek","year":"2005","journal-title":"Nat. Genet."},{"key":"2023051309020112200_btu811-B31","doi-asserted-by":"crossref","first-page":"e31587","DOI":"10.1371\/journal.pone.0031587","article-title":"Computational analysis of mRNA expression profiles identifies microRNA-29a\/c as predictor of colorectal cancer early recurrence","volume":"7","author":"Kuo","year":"2012","journal-title":"PLoS One"},{"key":"2023051309020112200_btu811-B32","doi-asserted-by":"crossref","first-page":"e1651","DOI":"10.1371\/journal.pone.0001651","article-title":"Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival","volume":"3","author":"Landi","year":"2008","journal-title":"PLoS One"},{"key":"2023051309020112200_btu811-B33","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1261\/rna.804508","article-title":"Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors","volume":"14","author":"Lee","year":"2008","journal-title":"RNA"},{"key":"2023051309020112200_btu811-B34","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","article-title":"Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets","volume":"120","author":"Lewis","year":"2005","journal-title":"Cell"},{"key":"2023051309020112200_btu811-B35","doi-asserted-by":"crossref","first-page":"e153","DOI":"10.1093\/nar\/gkr770","article-title":"Prioritizing human cancer microRNAs based on genes\u2019 functional consistency between microRNA and cancer","volume":"39","author":"Li","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023051309020112200_btu811-B36","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1471-2164-8-166","article-title":"Characterization of microRNA expression profiles in normal human tissues","volume":"8","author":"Liang","year":"2007","journal-title":"BMC Genomics"},{"key":"2023051309020112200_btu811-B37","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051309020112200_btu811-B38","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1038\/nature03315","article-title":"Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs","volume":"433","author":"Lim","year":"2005","journal-title":"Nature"},{"key":"2023051309020112200_btu811-B39","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/1471-2105-13-126","article-title":"Identifying dysregulated pathways in cancers from pathway interaction networks","volume":"13","author":"Liu","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023051309020112200_btu811-B40","doi-asserted-by":"crossref","first-page":"11","DOI":"10.4161\/rna.2.1.1552","article-title":"HuR: post-transcriptional paths to malignancy","volume":"2","author":"Lopez de Silanes","year":"2005","journal-title":"RNA Biol."},{"key":"2023051309020112200_btu811-B41","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03702","article-title":"MicroRNA expression profiles classify human cancers","volume":"435","author":"Lu","year":"2005","journal-title":"Nature"},{"key":"2023051309020112200_btu811-B42","doi-asserted-by":"crossref","first-page":"e3420","DOI":"10.1371\/journal.pone.0003420","article-title":"An analysis of human microRNA and disease associations","volume":"3","author":"Lu","year":"2008","journal-title":"PLoS One"},{"key":"2023051309020112200_btu811-B43","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1186\/1471-2105-10-295","article-title":"Accurate microRNA target prediction correlates with protein repression levels","volume":"10","author":"Maragkakis","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051309020112200_btu811-B44","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1476-4598-12-15","article-title":"MiR-29c is downregulated in gastric carcinomas and regulates cell proliferation by targeting RCC2","volume":"12","author":"Matsuo","year":"2013","journal-title":"Mol. Cancer"},{"key":"2023051309020112200_btu811-B45","doi-asserted-by":"crossref","first-page":"D619","DOI":"10.1093\/nar\/gkn863","article-title":"Reactome knowledgebase of human biological pathways and processes","volume":"37","author":"Matthews","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023051309020112200_btu811-B46","doi-asserted-by":"crossref","first-page":"3104","DOI":"10.1016\/j.ejca.2009.09.014","article-title":"MiRNA-29a regulates the expression of numerous proteins and reduces the invasiveness and proliferation of human carcinoma cell lines","volume":"45","author":"Muniyappa","year":"2009","journal-title":"Eur. J. Cancer"},{"key":"2023051309020112200_btu811-B47","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.canlet.2013.03.003","article-title":"MiR-145 functions as a tumor suppressor by directly targeting histone deacetylase 2 in liver cancer","volume":"335","author":"Noh","year":"2013","journal-title":"Cancer Lett"},{"key":"2023051309020112200_btu811-B48","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-1-60761-863-8_2","article-title":"Computational identification of miRNAs involved in cancer","volume":"676","author":"Oulas","year":"2011","journal-title":"Methods Mol. Biol."},{"key":"2023051309020112200_btu811-B65","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.prp.2009.11.006","article-title":"Gene expression patterns distinguish breast carcinomas from normal breast tissues: the Malaysian context","volume":"206","author":"Pau Ni","year":"2010","journal-title":"Pathol Res Pract"},{"key":"2023051309020112200_btu811-B49","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/nsmb.1533","article-title":"miR-29 miRNAs activate p53 by targeting p85 alpha and CDC42","volume":"16","author":"Park","year":"2009","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023051309020112200_btu811-B50","doi-asserted-by":"crossref","first-page":"9762","DOI":"10.1158\/0008-5472.CAN-07-2462","article-title":"MicroRNA let-7a down-regulates MYC and reverts MYC-induced growth in Burkitt lymphoma cells","volume":"67","author":"Sampson","year":"2007","journal-title":"Cancer Res."},{"key":"2023051309020112200_btu811-B51","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1261\/rna.2239606","article-title":"TarBase: a comprehensive database of experimentally supported animal microRNA targets","volume":"12","author":"Sethupathy","year":"2006","journal-title":"RNA"},{"key":"2023051309020112200_btu811-B52","doi-asserted-by":"crossref","first-page":"11400","DOI":"10.1073\/pnas.0704372104","article-title":"Let-7 expression defines two differentiation stages of cancer","volume":"104","author":"Shell","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023051309020112200_btu811-B53","doi-asserted-by":"crossref","first-page":"e13091","DOI":"10.1371\/journal.pone.0013091","article-title":"Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability","volume":"5","author":"Skrzypczak","year":"2010","journal-title":"PLoS One"},{"key":"2023051309020112200_btu811-B54","doi-asserted-by":"crossref","first-page":"3790","DOI":"10.1128\/MCB.05639-11","article-title":"Translational control of TOP2A influences doxorubicin efficacy","volume":"31","author":"Srikantan","year":"2011","journal-title":"Mol. Cell Biol."},{"key":"2023051309020112200_btu811-B55","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/1471-2164-8-140","article-title":"Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme","volume":"8","author":"Su","year":"2007","journal-title":"BMC Genomics"},{"key":"2023051309020112200_btu811-B56","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1158\/0008-5472.CAN-04-0637","article-title":"Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival","volume":"64","author":"Takamizawa","year":"2004","journal-title":"Cancer Res."},{"key":"2023051309020112200_btu811-B57","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/s12032-010-9766-y","article-title":"Upregulated INHBA expression is associated with poor survival in gastric cancer","volume":"29","author":"Wang","year":"2012","journal-title":"Med. Oncol."},{"key":"2023051309020112200_btu811-B58","doi-asserted-by":"crossref","first-page":"e3794","DOI":"10.1371\/journal.pone.0003794","article-title":"Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells","volume":"3","author":"Wu","year":"2008","journal-title":"PLoS One"},{"key":"2023051309020112200_btu811-B59","doi-asserted-by":"crossref","first-page":"3645","DOI":"10.3748\/wjg.v17.i31.3645","article-title":"Potentially predictive microRNAs of gastric cancer with metastasis to lymph node","volume":"17","author":"Wu","year":"2011","journal-title":"World J. Gastroenterol."},{"key":"2023051309020112200_btu811-B60","doi-asserted-by":"crossref","first-page":"e1002883","DOI":"10.1371\/journal.pcbi.1002883","article-title":"Important miRs of pathways in different tumor types","volume":"9","author":"Wuchty","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"2023051309020112200_btu811-B61","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.ccr.2006.01.025","article-title":"Unique microRNA molecular profiles in lung cancer diagnosis and prognosis","volume":"9","author":"Yanaihara","year":"2006","journal-title":"Cancer Cell"},{"key":"2023051309020112200_btu811-B62","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/1479-5876-12-66","article-title":"Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer","volume":"12","author":"Zhang","year":"2014","journal-title":"J. Transl. Med."},{"key":"2023051309020112200_btu811-B63","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1093\/nar\/gkn145","article-title":"Uncovering signal transduction networks from high-throughput data by integer linear programming","volume":"36","author":"Zhao","year":"2008","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1226\/50306111\/bioinformatics_31_8_1226.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1226\/50306111\/bioinformatics_31_8_1226.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T09:02:53Z","timestamp":1683968573000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/8\/1226\/212836"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12,12]]},"references-count":65,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2015,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu811","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,4,15]]},"published":{"date-parts":[[2014,12,12]]}}}