{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,15]],"date-time":"2024-09-15T20:52:41Z","timestamp":1726433561627},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: A rapid progression of esophageal squamous cell carcinoma (ESCC) causes a high mortality rate because of the propensity for metastasis driven by genetic and epigenetic alterations. The identification of prognostic biomarkers would help prevent or control metastatic progression. Expression analyses have been used to find such markers, but do not always validate in separate cohorts. Epigenetic marks, such as DNA methylation, are a potential source of more reliable and stable biomarkers. Importantly, the integration of both expression and epigenetic alterations is more likely to identify relevant biomarkers.<\/jats:p>\n               <jats:p>Results: We present a new analysis framework, using ESCC progression-associated gene regulatory network (GRN escc ), to identify differentially methylated CpG sites prognostic of ESCC progression. From the CpG loci differentially methylated in 50 tumor\u2013normal pairs, we selected 44 CpG loci most highly associated with survival and located in the promoters of genes more likely to belong to GRN escc . Using an independent ESCC cohort, we confirmed that 8\/10 of CpG loci in the promoter of GRN escc genes significantly correlated with patient survival. In contrast, 0\/10 CpG loci in the promoter genes outside the GRN escc were correlated with patient survival. We further characterized the GRN escc network topology and observed that the genes with methylated CpG loci associated with survival deviated from the center of mass and were less likely to be hubs in the GRN escc . We postulate that our analysis framework improves the identification of bona fide prognostic biomarkers from DNA methylation studies, especially with partial genome coverage.<\/jats:p>\n               <jats:p>Contact: \u00a0tsengsm@mail.ncku.edu.tw or ycw5798@mail.ncku.edu.tw<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu433","type":"journal-article","created":{"date-parts":[[2014,7,12]],"date-time":"2014-07-12T03:16:15Z","timestamp":1405134975000},"page":"3054-3061","source":"Crossref","is-referenced-by-count":11,"title":["Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression"],"prefix":"10.1093","volume":"30","author":[{"given":"Chun-Pei","family":"Cheng","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I-Ying","family":"Kuo","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hakan","family":"Alakus","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelly A.","family":"Frazer","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Harismendy","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi-Ching","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent S.","family":"Tseng","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"},{"name":"1 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, 2 Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA, 3 Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan, 4 Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093, USA, 5 Department of General, Visceral and Cancer Surgery, University of Cologne, K\u00f6ln, Germany, 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA, 7 Department of Pharmacology and 8 Institute of Medical Informatics, National Cheng Kung University, Tainan 701, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,7,10]]},"reference":[{"key":"2023012711574794000_btu433-B1","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1101\/gr.4410706","article-title":"High-throughput DNA methylation profiling using universal bead arrays","volume":"16","author":"Bibikova","year":"2006","journal-title":"Genome Res."},{"key":"2023012711574794000_btu433-B2","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1002\/jso.20569","article-title":"Staging of esophageal carcinoma: length of tumor and number of involved regional lymph nodes. Are these independent prognostic factors?","volume":"94","author":"Bollschweiler","year":"2006","journal-title":"J. Surg. Oncol."},{"key":"2023012711574794000_btu433-B3","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1093\/bioinformatics\/bth234","article-title":"Gene co-expression network topology provides a framework for molecular characterization of cellular state","volume":"20","author":"Carter","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012711574794000_btu433-B4","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway Commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012711574794000_btu433-B5","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/msb4100180","article-title":"Network-based classification of breast cancer metastasis","volume":"3","author":"Chuang","year":"2007","journal-title":"Mol. Syst. Biol."},{"volume-title":"Mathematical Methods of Statistics","year":"1946","author":"Cramer","key":"2023012711574794000_btu433-B6"},{"key":"2023012711574794000_btu433-B7","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/msb4100200","article-title":"A map of human cancer signaling","volume":"3","author":"Cui","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"2023012711574794000_btu433-B8","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: Database for annotation, visualization, and integrated discovery","volume":"4","author":"Dennis","year":"2003","journal-title":"Genome Biol."},{"key":"2023012711574794000_btu433-B9","first-page":"109","article-title":"The measure of association in a 2 \u00d7 2 table","volume":"126","author":"Edwards","year":"1963","journal-title":"J. R. Stat. Soc."},{"key":"2023012711574794000_btu433-B10","article-title":"Comparing top k lists","volume-title":"Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms","author":"Fagin","year":"2003"},{"key":"2023012711574794000_btu433-B11","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1093\/bioinformatics\/bts025","article-title":"Interactome-transcriptome integration for predicting distant metastasis in breast cancer","volume":"28","author":"Garcia","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711574794000_btu433-B12","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1002\/ijc.25764","article-title":"Interleukin-6 promotes tumorigenesis by altering DNA methylation in oral cancer cells","volume":"129","author":"Gasche","year":"2011","journal-title":"Int. J. Cancer"},{"key":"2023012711574794000_btu433-B13","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1016\/j.cell.2010.01.025","article-title":"Immunity, inflammation, and cancer","volume":"140","author":"Grivennikov","year":"2010","journal-title":"Cell"},{"key":"2023012711574794000_btu433-B14","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1007\/s10585-013-9597-2","article-title":"Decreased expression and aberrant methylation of Gadd45G is associated with tumor progression and poor prognosis in esophageal squamous cell carcinoma","volume":"30","author":"Guo","year":"2013","journal-title":"Clin. Exp. Metastasis"},{"key":"2023012711574794000_btu433-B15","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1245\/s10434-010-1393-5","article-title":"Identification and validation of DNA methylation markers to predict lymph node metastasis of esophageal squamous cell carcinomas","volume":"18","author":"Gyobu","year":"2011","journal-title":"Ann. Surg. Oncol."},{"issue":"Suppl. 1","key":"2023012711574794000_btu433-B16","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/bcr1988","article-title":"Mechanisms of metastasis","volume":"10","author":"Hunter","year":"2008","journal-title":"Breast Cancer Res."},{"key":"2023012711574794000_btu433-B17","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1097\/SLA.0b013e31826d8602","article-title":"LINE-1 hypomethylation is associated with a poor prognosis among patients with curatively resected esophageal squamous cell carcinoma","volume":"257","author":"Iwagami","year":"2013","journal-title":"Ann. Surg."},{"key":"2023012711574794000_btu433-B18","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1186\/1471-2164-11-669","article-title":"Global profiling of histone and DNA methylation reveals epigenetic-based regulation of gene expression during epithelial to mesenchymal transition in prostate cells","volume":"11","author":"Ke","year":"2010","journal-title":"BMC Genomics"},{"key":"2023012711574794000_btu433-B19","doi-asserted-by":"crossref","first-page":"e52973","DOI":"10.1371\/journal.pone.0052973","article-title":"Multi-analyte network markers for tumor prognosis","volume":"7","author":"Kim","year":"2012","journal-title":"PloS One"},{"key":"2023012711574794000_btu433-B20","doi-asserted-by":"crossref","first-page":"6658","DOI":"10.1158\/1078-0432.CCR-07-1178","article-title":"A promoter methylation pattern in the N-methyl-D-aspartate receptor 2B gene predicts poor prognosis in esophageal squamous cell carcinoma","volume":"13","author":"Kim","year":"2007","journal-title":"Clin. Cancer Res."},{"key":"2023012711574794000_btu433-B21","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1002\/int.4550070707","article-title":"Problems for knowledge discovery in databases and their treatment in the statistics interpreter explora","volume":"7","author":"Kl\u00f6sgen","year":"1992","journal-title":"Int. J. Intell. Syst."},{"key":"2023012711574794000_btu433-B22","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1145\/324133.324140","article-title":"Authoritative sources in a hyperlinked environment","volume":"46","author":"Kleinberg","year":"1999","journal-title":"J. ACM"},{"key":"2023012711574794000_btu433-B23","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1038\/jid.2011.27","article-title":"Malignant cutaneous T-cell lymphoma cells express IL-17 utilizing the Jak3\/Stat3 signaling pathway","volume":"131","author":"Krejsgaard","year":"2011","journal-title":"J. Invest. Dermatol."},{"key":"2023012711574794000_btu433-B24","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/nrc1045","article-title":"The power and the promise of DNA methylation markers","volume":"3","author":"Laird","year":"2003","journal-title":"Nat. Rev. Cancer"},{"key":"2023012711574794000_btu433-B25","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1016\/j.ejca.2006.01.021","article-title":"Aberrant methylation of fragile histidine triad gene is associated with poor prognosis in early stage esophageal squamous cell carcinoma","volume":"42","author":"Lee","year":"2006","journal-title":"Eur. J. Cancer"},{"key":"2023012711574794000_btu433-B26","doi-asserted-by":"crossref","first-page":"W123","DOI":"10.1093\/nar\/gks386","article-title":"SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data","volume":"40","author":"Li","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012711574794000_btu433-B27","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1172\/JCI31537","article-title":"A cytokine-mediated link between innate immunity, inflammation, and cancer","volume":"117","author":"Lin","year":"2007","journal-title":"J. Clin. Invest."},{"key":"2023012711574794000_btu433-B28","doi-asserted-by":"crossref","first-page":"4963","DOI":"10.1158\/0008-5472.CAN-04-3923","article-title":"PGP9.5 promoter methylation is an independent prognostic factor for esophageal squamous cell carcinoma","volume":"65","author":"Mandelker","year":"2005","journal-title":"Cancer Res."},{"key":"2023012711574794000_btu433-B29","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1038\/nsmb.2084","article-title":"Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition","volume":"18","author":"McDonald","year":"2011","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023012711574794000_btu433-B30","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/27.1.29","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"27","author":"Ogata","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023012711574794000_btu433-B31","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.socnet.2010.03.006","article-title":"Node centrality in weighted networks: generalizing degree and shortest paths","volume":"32","author":"Opsahl","year":"2010","journal-title":"Soc. Netw."},{"key":"2023012711574794000_btu433-B32","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1074\/mcp.M900227-MCP200","article-title":"Network-based Identification of novel cancer genes","volume":"9","author":"Ostlund","year":"2010","journal-title":"Mol. Cell Proteomics"},{"key":"2023012711574794000_btu433-B33","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/S0140-6736(12)60643-6","article-title":"Oesophageal carcinoma","volume":"381","author":"Pennathur","year":"2013","journal-title":"Lancet"},{"volume-title":"Discovery, Analysis, and Presentation of Strong Rules. Knowledge Discovery in Databases","year":"1991","author":"Piatetsky-Shapiro","key":"2023012711574794000_btu433-B34"},{"key":"2023012711574794000_btu433-B35","doi-asserted-by":"crossref","DOI":"10.1117\/12.339991","article-title":"An empirical evaluation of interest-level criteria","volume-title":"Data Mining and Knowledge Discovery: Theory, Tools, and Technology","author":"Sahar","year":"1999"},{"key":"2023012711574794000_btu433-B36","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkj109","article-title":"BioGRID: a general repository for interaction datasets","volume":"34","author":"Stark","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012711574794000_btu433-B37","doi-asserted-by":"crossref","first-page":"2127","DOI":"10.1002\/sim.5694","article-title":"Network-based regularization for matched case-control analysis of high-dimensional DNA methylation data","volume":"32","author":"Sun","year":"2013","journal-title":"Stat. Med."},{"key":"2023012711574794000_btu433-B38","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nrg2341","article-title":"DNA methylation landscapes: provocative insights from epigenomics","volume":"9","author":"Suzuki","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"2023012711574794000_btu433-B39","doi-asserted-by":"crossref","DOI":"10.1002\/9780470979174","volume-title":"Data Mining and Statistics for Decision Making","author":"Tuff\u00e9ry","year":"2011"},{"key":"2023012711574794000_btu433-B40","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1158\/0008-5472.CAN-08-2489","article-title":"Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors","volume":"69","author":"Vaissiere","year":"2009","journal-title":"Cancer Res."},{"key":"2023012711574794000_btu433-B41","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1056\/NEJMoa1112088","article-title":"Preoperative chemoradiotherapy for esophageal or junctional cancer","volume":"366","author":"van Hagen","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"2023012711574794000_btu433-B42","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1002\/art.37819","article-title":"Tumor necrosis factor alpha- and interleukin-1beta-dependent induction of CCL3 expression by nucleus pulposus cells promotes macrophage migration through CCR1","volume":"65","author":"Wang","year":"2013","journal-title":"Arthritis Rheum."},{"key":"2023012711574794000_btu433-B43","doi-asserted-by":"crossref","first-page":"14138","DOI":"10.1073\/pnas.1307242110","article-title":"Distinctive topology of age-associated epigenetic drift in the human interactome","volume":"110","author":"West","year":"2013","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711574794000_btu433-B44","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1145\/956750.956782","article-title":"Algorithms for estimating relative importance in networks","volume-title":"Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining","author":"White","year":"2003"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/21\/3054\/48931064\/bioinformatics_30_21_3054.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/21\/3054\/48931064\/bioinformatics_30_21_3054.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:52:50Z","timestamp":1674823970000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/21\/3054\/2422165"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,7,10]]},"references-count":44,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2014,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu433","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2014,11,1]]},"published":{"date-parts":[[2014,7,10]]}}}