{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T10:16:12Z","timestamp":1779272172211,"version":"3.51.4"},"reference-count":102,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2017,1,23]],"date-time":"2017-01-23T00:00:00Z","timestamp":1485129600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation (US)","doi-asserted-by":"crossref","award":["CNS1358939"],"award-info":[{"award-number":["CNS1358939"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation (US)","doi-asserted-by":"crossref","award":["CRI 1305302"],"award-info":[{"award-number":["CRI 1305302"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0170025","type":"journal-article","created":{"date-parts":[[2017,1,23]],"date-time":"2017-01-23T19:12:07Z","timestamp":1485198727000},"page":"e0170025","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Underexpression of Specific Interferon Genes Is Associated with Poor Prognosis of Melanoma"],"prefix":"10.1371","volume":"12","author":[{"given":"Aamir","family":"Zainulabadeen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip","family":"Yao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5902-6238","authenticated-orcid":true,"given":"Habil","family":"Zare","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2017,1,23]]},"reference":[{"issue":"1","key":"ref1","first-page":"5","article-title":"Cancer statistics, 2015","volume":"65","author":"RL Siegel","year":"2015","journal-title":"CA: a cancer journal for clinicians"},{"issue":"14","key":"ref2","doi-asserted-by":"crossref","first-page":"2452","DOI":"10.1200\/JCO.2009.27.1627","article-title":"Multivariate analysis of prognostic factors among 2,313 patients with stage III melanoma: comparison of nodal micrometastases versus macrometastases","volume":"28","author":"CM Balch","year":"2010","journal-title":"Journal of Clinical Oncology"},{"issue":"36","key":"ref3","doi-asserted-by":"crossref","first-page":"6199","DOI":"10.1200\/JCO.2009.23.4799","article-title":"Final version of 2009 AJCC melanoma staging and classification","volume":"27","author":"CM Balch","year":"2009","journal-title":"Journal of clinical oncology"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1158\/1078-0432.CCR-13-3316","article-title":"Development of a prognostic genetic signature to predict the metastatic risk associated with cutaneous melanoma","volume":"21","author":"P Gerami","year":"2015","journal-title":"Clinical Cancer Research"},{"key":"ref5","first-page":"1","article-title":"Prediction is Difficult, Especially About the Future: Clinical Prognostic Tools in Melanoma","author":"VK Sondak","year":"2016","journal-title":"Annals of surgical oncology"},{"issue":"9","key":"ref6","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1200\/JCO.2006.08.1463","article-title":"Identification of high-risk patients among those diagnosed with thin cutaneous melanomas","volume":"25","author":"PA Gimotty","year":"2007","journal-title":"Journal of Clinical Oncology"},{"issue":"13","key":"ref7","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1056\/NEJMoa060992","article-title":"Sentinel-node biopsy or nodal observation in melanoma","volume":"355","author":"DL Morton","year":"2006","journal-title":"New England Journal of Medicine"},{"key":"ref8","article-title":"Inflammatory Marker Testing Identifies CD74 Expression in Melanoma Tumor Cells, and its Expression Associates with Favorable Survival for Stage III Melanoma","author":"S Ekmekcioglu","year":"2016","journal-title":"Clinical Cancer Research"},{"issue":"4","key":"ref9","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.jamcollsurg.2015.12.042","article-title":"Molecular Staging of Sentinel Lymph Nodes Identifies Melanoma Patients at Increased Risk of Nodal Recurrence","volume":"222","author":"CW Kimbrough","year":"2016","journal-title":"Journal of the American College of Surgeons"},{"issue":"23","key":"ref10","doi-asserted-by":"crossref","first-page":"4108","DOI":"10.1002\/cncr.29634","article-title":"Revisiting determinants of prognosis in cutaneous melanoma","volume":"121","author":"SA Weiss","year":"2015","journal-title":"Cancer"},{"issue":"1","key":"ref11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-8-73","article-title":"Diagnostic and prognostic gene expression signatures in 177 soft tissue sarcomas: hypoxia-induced transcription profile signifies metastatic potential","volume":"8","author":"P Francis","year":"2007","journal-title":"BMC genomics"},{"issue":"27","key":"ref12","doi-asserted-by":"crossref","first-page":"2817","DOI":"10.1056\/NEJMoa041588","article-title":"A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer","volume":"351","author":"S Paik","year":"2004","journal-title":"New England Journal of Medicine"},{"key":"ref13","article-title":"A multigene predictor of outcome in glioblastoma","author":"H Colman","year":"2009","journal-title":"Neuro-oncology"},{"issue":"8","key":"ref14","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1093\/jnci\/95.8.598","article-title":"Using gene expression ratios to predict outcome among patients with mesothelioma","volume":"95","author":"GJ Gordon","year":"2003","journal-title":"Journal of the National Cancer Institute"},{"issue":"20","key":"ref15","doi-asserted-by":"crossref","first-page":"7205","DOI":"10.1158\/0008-5472.CAN-04-1750","article-title":"Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death","volume":"64","author":"MD Onken","year":"2004","journal-title":"Cancer research"},{"issue":"2","key":"ref16","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.pathol.2015.12.004","article-title":"Molecular techniques for predicting behaviour in melanocytic neoplasms","volume":"48","author":"CY Lee","year":"2016","journal-title":"Pathology"},{"issue":"6","key":"ref17","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1016\/j.jaad.2015.02.1140","article-title":"Practical application of new technologies for melanoma diagnosis: Part II. Molecular approaches","volume":"72","author":"J March","year":"2015","journal-title":"Journal of the American Academy of Dermatology"},{"issue":"4","key":"ref18","doi-asserted-by":"crossref","first-page":"475","DOI":"10.6004\/jnccn.2016.0052","article-title":"Molecular Profiling in Cutaneous Melanoma","volume":"14","author":"AL Ji","year":"2016","journal-title":"Journal of the National Comprehensive Cancer Network"},{"issue":"4","key":"ref19","doi-asserted-by":"crossref","first-page":"461","DOI":"10.2353\/jmoldx.2010.090220","article-title":"An accurate, clinically feasible multi-gene expression assay for predicting metastasis in uveal melanoma","volume":"12","author":"MD Onken","year":"2010","journal-title":"The Journal of Molecular Diagnostics"},{"issue":"8","key":"ref20","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1016\/j.ophtha.2012.02.017","article-title":"Collaborative Ocular Oncology Group report number 1: prospective validation of a multi-gene prognostic assay in uveal melanoma","volume":"119","author":"MD Onken","year":"2012","journal-title":"Ophthalmology"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1158\/1078-0432.CCR-06-1820","article-title":"Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues","volume":"13","author":"J Jaeger","year":"2007","journal-title":"Clinical cancer research"},{"issue":"6795","key":"ref22","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/35020115","article-title":"Molecular classification of cutaneous malignant melanoma by gene expression profiling","volume":"406","author":"M Bittner","year":"2000","journal-title":"Nature"},{"issue":"17","key":"ref23","doi-asserted-by":"crossref","first-page":"6092","DOI":"10.1073\/pnas.0501564102","article-title":"The gene expression signatures of melanoma progression","volume":"102","author":"C Haqq","year":"2005","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"8","key":"ref24","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.1002\/ijc.24899","article-title":"Altered molecular pathways in melanocytic lesions","volume":"126","author":"M Scatolini","year":"2010","journal-title":"International Journal of Cancer"},{"issue":"9","key":"ref25","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.4161\/cbt.4.9.2165","article-title":"Whole-genome expression profiling of the melanoma progression pathway reveals marked molecular differences between nevi\/melanoma in situ and advanced-stage melanomas","volume":"4","author":"AP Smith","year":"2005","journal-title":"Cancer biology & therapy"},{"issue":"12","key":"ref26","doi-asserted-by":"crossref","first-page":"2264","DOI":"10.1038\/sj.onc.1207337","article-title":"Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome","volume":"23","author":"AT Weeraratna","year":"2004","journal-title":"Oncogene"},{"issue":"7","key":"ref27","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1093\/jnci\/djj103","article-title":"Gene expression profiling of primary cutaneous melanoma and clinical outcome","volume":"98","author":"V Winnepenninckx","year":"2006","journal-title":"Journal of the National Cancer Institute"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","year":"2000","journal-title":"Nature Genetics"},{"issue":"5","key":"ref29","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1016\/j.jaad.2015.01.009","article-title":"Gene expression profiling for molecular staging of cutaneous melanoma in patients undergoing sentinel lymph node biopsy","volume":"72","author":"P Gerami","year":"2015","journal-title":"Journal of the American Academy of Dermatology"},{"key":"ref30","first-page":"1","article-title":"Clinical impact of a 31-gene expression profile test for cutaneous melanoma in 156 prospectively and consecutively tested patients","author":"AC Berger","year":"2016","journal-title":"Current medical research and opinion"},{"issue":"11","key":"ref31","doi-asserted-by":"crossref","first-page":"782","DOI":"10.3111\/13696998.2014.950421","article-title":"Budget impact analysis of a novel gene expression assay for the diagnosis of malignant melanoma","volume":"17","author":"DS Cassarino","year":"2014","journal-title":"Journal of medical economics"},{"key":"ref32","first-page":"1","article-title":"Critical assessment of clinical prognostic tools in melanoma","author":"AL Mahar","year":"2016","journal-title":"Annals of surgical oncology"},{"issue":"7","key":"ref33","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1016\/j.cell.2015.05.044","article-title":"Genomic classification of cutaneous melanoma","volume":"161","year":"2015","journal-title":"Cell"},{"key":"ref34","unstructured":"Zare H, et al. Pigengene: Computing and using eigengenes. Bioconductor; 2016. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/bioconductor.org\/packages\/devel\/bioc\/html\/Pigengene.html\" xlink:type=\"simple\">https:\/\/bioconductor.org\/packages\/devel\/bioc\/html\/Pigengene.html<\/ext-link>."},{"issue":"20","key":"ref35","doi-asserted-by":"crossref","first-page":"7234","DOI":"10.1158\/1078-0432.CCR-05-0683","article-title":"Novel genes associated with malignant melanoma but not benign melanocytic lesions","volume":"11","author":"D Talantov","year":"2005","journal-title":"Clinical Cancer Research"},{"issue":"1","key":"ref36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1755-8794-1-13","article-title":"The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis","volume":"1","author":"AI Riker","year":"2008","journal-title":"BMC medical genomics"},{"issue":"4","key":"ref37","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1089\/cbr.2008.0473","article-title":"Increased expression of the tumor suppressor PLZF is a continuous predictor of long-term survival in malignant melanoma patients","volume":"23","author":"G Brunner","year":"2008","journal-title":"Cancer biotherapy & radiopharmaceuticals"},{"issue":"2","key":"ref38","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1007\/s00432-012-1322-z","article-title":"A nine-gene signature predicting clinical outcome in cutaneous melanoma","volume":"139","author":"G Brunner","year":"2013","journal-title":"Journal of cancer research and clinical oncology"},{"issue":"13","key":"ref39","doi-asserted-by":"crossref","first-page":"11683","DOI":"10.18632\/oncotarget.3549","article-title":"Independent replication of a melanoma subtype gene signature and evaluation of its prognostic value and biological correlates in a population cohort","volume":"6","author":"J Nsengimana","year":"2015","journal-title":"Oncotarget"},{"key":"ref40","article-title":"Molecular stratification of metastatic melanoma using gene expression profiling: prediction of survival outcome and benefit from molecular targeted therapy","author":"H Cirenajwis","year":"2015","journal-title":"Oncotarget"},{"key":"ref41","article-title":"TCGA2STAT: simple TCGA data access for integrated statistical analysis in R","author":"YW Wan","year":"2015","journal-title":"Bioinformatics"},{"issue":"5","key":"ref42","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/nbt.2862","article-title":"Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms","volume":"32","author":"R Patro","year":"2014","journal-title":"Nature biotechnology"},{"issue":"24","key":"ref43","doi-asserted-by":"crossref","first-page":"1893","DOI":"10.1093\/jnci\/81.24.1893","article-title":"Model predicting survival in stage I melanoma based on tumor progression","volume":"81","author":"WH Clark","year":"1989","journal-title":"Journal of the National Cancer Institute"},{"key":"ref44","first-page":"358","article-title":"Spearman rank correlation coefficient","author":"WW Daniel","year":"1990"},{"issue":"11","key":"ref45","doi-asserted-by":"crossref","first-page":"e50411","DOI":"10.1371\/journal.pone.0050411","article-title":"Evaluation of gene association methods for coexpression network construction and biological knowledge discovery","volume":"7","author":"S Kumari","year":"2012","journal-title":"PloS one"},{"issue":"3","key":"ref46","first-page":"69","article-title":"A guide to appropriate use of Correlation coefficient in medical research","volume":"24","author":"M Mukaka","year":"2012","journal-title":"Malawi Medical Journal"},{"issue":"3","key":"ref47","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1016\/j.cell.2013.03.030","article-title":"Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer\u2019s disease","volume":"153","author":"B Zhang","year":"2013","journal-title":"Cell"},{"issue":"10","key":"ref48","doi-asserted-by":"crossref","first-page":"3238","DOI":"10.1200\/JCO.1999.17.10.3238","article-title":"Prognostic significance of occult metastases detected by sentinel lymphadenectomy and reverse transcriptase\u2013polymerase chain reaction in early-stage melanoma patients","volume":"17","author":"PJ Bostick","year":"1999","journal-title":"Journal of clinical oncology"},{"issue":"9","key":"ref49","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1001\/archsurg.139.9.961","article-title":"Contemporary surgical treatment of advanced-stage melanoma","volume":"139","author":"R Essner","year":"2004","journal-title":"Archives of surgery"},{"issue":"7","key":"ref50","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1007\/BF02574479","article-title":"Multivariate prognostic model for patients with thick cutaneous melanoma: importance of sentinel lymph node status","volume":"9","author":"CR Ferrone","year":"2002","journal-title":"Annals of Surgical Oncology"},{"issue":"11","key":"ref51","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1200\/JCO.1998.16.11.3584","article-title":"Downregulation of transcription factor AP-2 predicts poor survival in stage I cutaneous malignant melanoma","volume":"16","author":"JM Karjalainen","year":"1998","journal-title":"Journal of clinical oncology"},{"key":"ref52","article-title":"ArrayExpress update x2014;simplifying data submissions","author":"N Kolesnikov","year":"2014","journal-title":"Nucleic acids research"},{"issue":"D1","key":"ref53","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2013update","volume":"41","author":"T Barrett","year":"2013","journal-title":"Nucleic acids research"},{"issue":"14","key":"ref54","doi-asserted-by":"crossref","first-page":"1846","DOI":"10.1093\/bioinformatics\/btm254","article-title":"GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor","volume":"23","author":"S Davis","year":"2007","journal-title":"Bioinformatics"},{"issue":"1","key":"ref55","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":"P Langfelder","year":"2008","journal-title":"BMC bioinformatics"},{"key":"ref56","article-title":"Principal component analysis","author":"I Jolliffe","year":"2002"},{"issue":"47","key":"ref57","doi-asserted-by":"crossref","first-page":"17973","DOI":"10.1073\/pnas.0605938103","article-title":"Conservation and evolution of gene coexpression networks in human and chimpanzee brains","volume":"103","author":"MC Oldham","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"5","key":"ref58","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v039.i05","article-title":"Regularization paths for Cox\u2019s proportional hazards model via coordinate descent","volume":"39","author":"N Simon","year":"2011","journal-title":"Journal of statistical software"},{"key":"ref59","first-page":"527","article-title":"Breakthroughs in statistics","author":"DR Cox","year":"1992"},{"issue":"13","key":"ref60","doi-asserted-by":"crossref","first-page":"3001","DOI":"10.1093\/bioinformatics\/bti422","article-title":"Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data","volume":"21","author":"J Gui","year":"2005","journal-title":"Bioinformatics"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression shrinkage and selection via the lasso","author":"R Tibshirani","year":"1996","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"key":"ref62","article-title":"The statistical analysis of failure time data","volume":"vol. 360","author":"JD Kalbfleisch","year":"2011"},{"key":"ref63","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3294-8","article-title":"Modeling survival data: extending the Cox model","author":"TM Therneau","year":"2000"},{"issue":"282","key":"ref64","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1080\/01621459.1958.10501452","article-title":"Nonparametric estimation from incomplete observations","volume":"53","author":"EL Kaplan","year":"1958","journal-title":"Journal of the American statistical association"},{"issue":"4","key":"ref65","first-page":"719","article-title":"Statistical aspects of the analysis of data from retrospective studies","volume":"22","author":"N Mantel","year":"1959","journal-title":"J natl cancer inst"},{"key":"ref66","article-title":"InnateDB: systems biology of innate immunity and beyond\u2013recent updates and continuing curation","author":"K Breuer","year":"2012","journal-title":"Nucleic acids research"},{"issue":"D1","key":"ref67","doi-asserted-by":"crossref","first-page":"D472","DOI":"10.1093\/nar\/gkt1102","article-title":"The Reactome pathway knowledgebase","volume":"42","author":"D Croft","year":"2014","journal-title":"Nucleic acids research"},{"issue":"5","key":"ref68","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/nrc1881","article-title":"Ubiquitin ligases: cell-cycle control and cancer","volume":"6","author":"KI Nakayama","year":"2006","journal-title":"Nature Reviews Cancer"},{"issue":"4","key":"ref69","doi-asserted-by":"crossref","first-page":"e34247","DOI":"10.1371\/journal.pone.0034247","article-title":"Cell cycle gene networks are associated with melanoma prognosis","volume":"7","author":"L Wang","year":"2012","journal-title":"PloS one"},{"issue":"D1","key":"ref70","doi-asserted-by":"crossref","first-page":"D336","DOI":"10.1093\/nar\/gkv1194","article-title":"PANTHER version 10: expanded protein families and functions, and analysis tools","volume":"44","author":"H Mi","year":"2016","journal-title":"Nucleic acids research"},{"key":"ref71","article-title":"Etude comparative de la distribution florale dans une portion des Alpes et du Jura","author":"P Jaccard","year":"1901"},{"key":"ref72","article-title":"Elementary mathematical theory of classification and prediction","author":"TT Tanimoto","year":"1958"},{"issue":"3","key":"ref73","first-page":"163","article-title":"Evaluation of survival data and two new rank order statistics arising in its consideration","volume":"50","author":"N Mantel","year":"1966","journal-title":"Cancer chemotherapy reports Part 1"},{"issue":"8","key":"ref74","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1038\/jid.2014.85","article-title":"Dissection of Immune Gene Networks in Primary Melanoma Tumors Critical for Antitumor Surveillance of Patients with Stage II\u2013III Resectable Disease","volume":"134","author":"S Sivendran","year":"2014","journal-title":"Journal of Investigative Dermatology"},{"key":"ref75","first-page":"377","article-title":"Inflammation and Cancer","author":"S Deivendran","year":"2014"},{"issue":"1","key":"ref76","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1002\/pbc.23339","article-title":"Bone marrow of neuroblastoma patients shows downregulation of CXCL12 expression and presence of IFN signature","volume":"59","author":"P Scaruffi","year":"2012","journal-title":"Pediatric blood & cancer"},{"issue":"1","key":"ref77","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.cyto.2014.07.240","article-title":"S-20: Exploiting the type-1 interferon pathway as a biomarker and therapeutic target for metastatic cancer","volume":"70","author":"J Rautela","year":"2014","journal-title":"Cytokine"},{"issue":"10","key":"ref78","doi-asserted-by":"crossref","first-page":"e111061","DOI":"10.1371\/journal.pone.0111061","article-title":"Single nucleotide polymorphisms within interferon signaling pathway genes are associated with colorectal cancer susceptibility and survival","volume":"9","author":"S Lu","year":"2014","journal-title":"PloS one"},{"issue":"11","key":"ref79","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.18632\/oncotarget.1542","article-title":"Alterations of immune response of non-small cell lung cancer with azacytidine","volume":"4","author":"J Wrangle","year":"2013","journal-title":"Oncotarget"},{"issue":"1","key":"ref80","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.virol.2012.11.014","article-title":"Resistance of pancreatic cancer cells to oncolytic vesicular stomatitis virus: role of type I interferon signaling","volume":"436","author":"M Moerdyk-Schauwecker","year":"2013","journal-title":"Virology"},{"issue":"5","key":"ref81","doi-asserted-by":"crossref","first-page":"e176","DOI":"10.1371\/journal.pmed.0040176","article-title":"Down-regulation of the interferon signaling pathway in T lymphocytes from patients with metastatic melanoma","volume":"4","author":"RJ Critchley-Thorne","year":"2007","journal-title":"PLoS Med"},{"issue":"15","key":"ref82","doi-asserted-by":"crossref","first-page":"5270","DOI":"10.1158\/0008-5472.CAN-04-0731","article-title":"Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas","volume":"64","author":"K Hoek","year":"2004","journal-title":"Cancer research"},{"issue":"57","key":"ref83","doi-asserted-by":"crossref","first-page":"8741","DOI":"10.1038\/sj.onc.1205987","article-title":"Neoplastic progression in melanoma and colon cancer is associated with increased expression and activity of the interferon-inducible protein kinase, PKR","volume":"21","author":"SH Kim","year":"2002","journal-title":"Oncogene"},{"issue":"5","key":"ref84","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1016\/j.molcel.2014.12.030","article-title":"Interferon <italic>\u03b1<\/italic>\/<italic>\u03b2<\/italic> enhances the cytotoxic response of MEK inhibition in melanoma","volume":"57","author":"O Litvin","year":"2015","journal-title":"Molecular cell"},{"issue":"3","key":"ref85","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1007\/s12094-008-0170-4","article-title":"Uveal vs. cutaneous melanoma. Origins and causes of the differences","volume":"10","author":"C Belmar-Lopez","year":"2008","journal-title":"Clinical and Translational Oncology"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/B978-0-12-397927-8.00011-7","article-title":"Intratumoral heterogeneity as a therapy resistance mechanism: role of melanoma subpopulations","volume":"65","author":"R Somasundaram","year":"2012","journal-title":"Advances in pharmacology (San Diego, Calif)"},{"issue":"1","key":"ref87","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1755-8794-6-40","article-title":"Intratumoral genetic heterogeneity in metastatic melanoma is accompanied by variation in malignant behaviors","volume":"6","author":"M Anaka","year":"2013","journal-title":"BMC medical genomics"},{"issue":"10","key":"ref88","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1038\/aps.2015.92","article-title":"Intra-tumor heterogeneity of cancer cells and its implications for cancer treatment","volume":"36","author":"Xx Sun","year":"2015","journal-title":"Acta Pharmacologica Sinica"},{"issue":"6282","key":"ref89","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"I Tirosh","year":"2016","journal-title":"Science"},{"issue":"7","key":"ref90","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nri3845","article-title":"Type I interferons in anticancer immunity","volume":"15","author":"L Zitvogel","year":"2015","journal-title":"Nature Reviews Immunology"},{"issue":"5","key":"ref91","doi-asserted-by":"crossref","first-page":"1740","DOI":"10.1016\/j.celrep.2014.04.055","article-title":"High-definition reconstruction of clonal composition in cancer","volume":"7","author":"A Fischer","year":"2014","journal-title":"Cell reports"},{"key":"ref92","article-title":"Nature methods","author":"A Roth","year":"2014"},{"issue":"7","key":"ref93","doi-asserted-by":"crossref","first-page":"e1003703","DOI":"10.1371\/journal.pcbi.1003703","article-title":"Inferring clonal composition from multiple sections of a breast cancer","volume":"10","author":"H Zare","year":"2014","journal-title":"PLoS computational biology"},{"issue":"20","key":"ref94","doi-asserted-by":"crossref","first-page":"4191","DOI":"10.1182\/blood-2012-05-433540","article-title":"Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns","volume":"120","author":"A Schuh","year":"2012","journal-title":"Blood"},{"key":"ref95","doi-asserted-by":"crossref","unstructured":"Marass F, Mouliere F, Yuan K, Rosenfeld N, Markowetz F. A phylogenetic latent feature model for clonal deconvolution. arXiv preprint arXiv:160401715. 2016;.","DOI":"10.1214\/16-AOAS986"},{"key":"ref96","doi-asserted-by":"crossref","unstructured":"Matsui Y, Niida A, Uchi R, Mimori K, Miyano S, Shimamura T. phyC: Clustering cancer evolutionary trees. bioRxiv. 2016;p. 069302.","DOI":"10.1101\/069302"},{"issue":"37","key":"ref97","doi-asserted-by":"crossref","first-page":"E5528","DOI":"10.1073\/pnas.1522203113","article-title":"Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing","volume":"113","author":"Y Jiang","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.coi.2016.06.006","article-title":"High-throughput genomic profiling of tumor-infiltrating leukocytes","volume":"41","author":"AM Newman","year":"2016","journal-title":"Current Opinion in Immunology"},{"issue":"17","key":"ref99","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1093\/bioinformatics\/btt351","article-title":"CellMix: a comprehensive toolbox for gene expression deconvolution","volume":"29","author":"R Gaujoux","year":"2013","journal-title":"Bioinformatics"},{"key":"ref100","article-title":"CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations","author":"M Chikina","year":"2015","journal-title":"Bioinformatics"},{"key":"ref101","doi-asserted-by":"crossref","unstructured":"Houseman EA, Kile ML, Christiani DC, Ince TA, Kelsey KT, Marsit CJ. Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. bioRxiv. 2016;p. 037671.","DOI":"10.1186\/s12859-016-1140-4"},{"issue":"2","key":"ref102","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2000-1-2-research0003","article-title":"Gene shaving as a method for identifying distinct sets of genes with similar expression patterns","volume":"1","author":"T Hastie","year":"2000","journal-title":"Genome Biol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0170025","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T16:55:15Z","timestamp":1589043315000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0170025"}},"subtitle":[],"editor":[{"given":"Roger","family":"Chammas","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,1,23]]},"references-count":102,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,1,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0170025","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,23]]}}}