{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T11:38:15Z","timestamp":1772365095249,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006290","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,7,11]],"date-time":"2018-07-11T00:00:00Z","timestamp":1531267200000}}],"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2018,6,28]],"date-time":"2018-06-28T00:00:00Z","timestamp":1530144000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DGE 1148900"],"award-info":[{"award-number":["DGE 1148900"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ABI-0850063"],"award-info":[{"award-number":["ABI-0850063"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM076275"],"award-info":[{"award-number":["GM076275"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA208148"],"award-info":[{"award-number":["CA208148"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"State of Nebraska","award":["Nebraska Research Initiative Grant"],"award-info":[{"award-number":["Nebraska Research Initiative Grant"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006290","type":"journal-article","created":{"date-parts":[[2018,6,28]],"date-time":"2018-06-28T18:30:47Z","timestamp":1530210647000},"page":"e1006290","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":45,"title":["Two critical positions in zinc finger domains are heavily mutated in three human cancer types"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0724-218X","authenticated-orcid":true,"given":"Daniel","family":"Munro","sequence":"first","affiliation":[]},{"given":"Dario","family":"Ghersi","sequence":"additional","affiliation":[]},{"given":"Mona","family":"Singh","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2018,6,28]]},"reference":[{"issue":"7291","key":"ref1","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"TJ Hudson","year":"2010","journal-title":"Nature"},{"issue":"1A","key":"ref2","first-page":"A68","article-title":"The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge","volume":"19","author":"K Tomczak","year":"2015","journal-title":"Contemp Oncol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature12213","article-title":"Mutational heterogeneity in cancer and the search for new cancer-associated genes","volume":"499","author":"MS Lawrence","year":"2013","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/1476-4598-10-54","article-title":"The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors","volume":"10","author":"H Stehr","year":"2011","journal-title":"Mol Cancer"},{"issue":"6","key":"ref5","doi-asserted-by":"crossref","first-page":"e66273","DOI":"10.1371\/journal.pone.0066273","article-title":"Cancer missense mutations alter binding properties of proteins and their interaction networks","volume":"8","author":"H Nishi","year":"2013","journal-title":"PLOS ONE"},{"issue":"3","key":"ref6","doi-asserted-by":"crossref","first-page":"e18","DOI":"10.1093\/nar\/gkt1305","article-title":"Interaction-based discovery of functionally important genes in cancers","volume":"42","author":"D Ghersi","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"6797","key":"ref7","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/35021093","article-title":"Molecular portraits of human breast tumours","volume":"406","author":"CM Perou","year":"2000","journal-title":"Nature"},{"issue":"5015","key":"ref8","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1126\/science.1905840","article-title":"p53 mutations in human cancers","volume":"253","author":"M Hollstein","year":"1991","journal-title":"Science"},{"issue":"1","key":"ref9","doi-asserted-by":"crossref","first-page":"e55119","DOI":"10.1371\/journal.pone.0055119","article-title":"The spectrum of SWI\/SNF mutations, ubiquitous in human cancers","volume":"8","author":"AH Shain","year":"2013","journal-title":"PLOS ONE"},{"issue":"7418","key":"ref10","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumors","volume":"490","year":"2012","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","DOI":"10.1038\/nrg2538","article-title":"A census of human transcription factors: function, expression and evolution","volume":"10","author":"J Vaquerizas","year":"2009","journal-title":"Nature Review Genetics"},{"issue":"10","key":"ref12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2003-4-10-231","article-title":"KRAB-containing zinc-finger repressor proteins","volume":"4","author":"R Urrutia","year":"2003","journal-title":"Genome Biology"},{"issue":"4","key":"ref13","doi-asserted-by":"crossref","first-page":"268","DOI":"10.2174\/13892029113149990002","article-title":"KRAB-Zinc finger proteins: A repressor family displaying multiple biological functions","volume":"14","author":"A Lupo","year":"2013","journal-title":"Current Genomics"},{"issue":"3","key":"ref14","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1093\/gbe\/evu030","article-title":"Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies","volume":"6","author":"H Liu","year":"2014","journal-title":"Genome Biol Evol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1038\/nature07844","article-title":"Embryonic stem cells use ZFP809 to silence retroviral DNAs","volume":"458","author":"D Wolf","year":"2009","journal-title":"Nature"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nature13760","article-title":"An evolutionary arms race between KRAB zinc-finger genes ZNF91\/93 and SVA\/L1 retrotransposons","volume":"516","author":"F Jacobs","year":"2014","journal-title":"Nature"},{"issue":"12","key":"ref17","doi-asserted-by":"crossref","first-page":"1742","DOI":"10.1101\/gr.209643.116","article-title":"Multiparameter functional diversity of human C2H2 zinc finger proteins","volume":"26","author":"FW Schmitges","year":"2016","journal-title":"Genome Research"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/nature21683","article-title":"KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks","volume":"543","author":"M Imbeault","year":"2017","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.cell.2012.06.013","article-title":"Cancer epigenetics: from mechanism to therapy","volume":"150","author":"M Dawson","year":"2012","journal-title":"Cell"},{"issue":"7","key":"ref20","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nrc.2017.35","article-title":"Transposable elements in cancer","volume":"17","author":"KH Burns","year":"2017","journal-title":"Nature Reviews Cancer"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev.biophys.29.1.183","article-title":"DNA recognition by Cys2His2 zinc finger proteins","volume":"29","author":"S Wolfe","year":"2000","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"3","key":"ref22","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.cels.2015.08.014","article-title":"Pan-cancer analysis of mutation hotspots in protein domains","volume":"1","author":"M Miller","year":"2015","journal-title":"Cell Systems"},{"issue":"19","key":"ref23","doi-asserted-by":"crossref","first-page":"9147","DOI":"10.1093\/nar\/gkv919","article-title":"A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity","volume":"43","author":"M Garton","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"5129","key":"ref24","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1126\/science.8378770","article-title":"Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers","volume":"261","author":"NP Pavletich","year":"1993","journal-title":"Science"},{"issue":"23","key":"ref25","doi-asserted-by":"crossref","first-page":"9374","DOI":"10.1016\/S0021-9258(17)37118-1","article-title":"Mutations in the zinc-finger region of the yeast regulatory protein ADR1 affect both DNA binding and transcriptional activation","volume":"269","author":"WJ Cook","year":"1994","journal-title":"J Biol Chem"},{"issue":"2","key":"ref26","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/ng.2503","article-title":"Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas","volume":"45","author":"C Palles","year":"2013","journal-title":"Nat Genet"},{"issue":"14","key":"ref27","doi-asserted-by":"crossref","first-page":"2820","DOI":"10.1093\/hmg\/ddt131","article-title":"DNA polymerase epsilon and delta exonuclease domain mutations in endometrial cancer","volume":"22","author":"DN Church","year":"2013","journal-title":"Hum Mol Genet"},{"issue":"7407","key":"ref28","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/nature11252","article-title":"Comprehensive molecular characterization of human colon and rectal cancer","volume":"487","year":"2012","journal-title":"Nature"},{"issue":"7447","key":"ref29","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/nature12113","article-title":"Integrated genomic characterization of endometrial carcinoma","volume":"497","year":"2013","journal-title":"Nature"},{"issue":"2","key":"ref30","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/j.cell.2012.06.024","article-title":"A landscape of driver mutations in melanoma","volume":"150","author":"E Hodis","year":"2012","journal-title":"Cell"},{"issue":"7","key":"ref31","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"},{"issue":"D1","key":"ref32","doi-asserted-by":"crossref","first-page":"D470","DOI":"10.1093\/nar\/gku1204","article-title":"The BioGRID interaction database: 2015 update","volume":"43","author":"A Chatr-Aryamontri","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"ref33","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1038\/nrc1186","article-title":"The role of Notch in tumorigenesis: oncogene or tumour suppressor?","volume":"3","author":"F Radtke","year":"2003","journal-title":"Nature Reviews Cancer"},{"issue":"3","key":"ref34","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nrc1299","article-title":"A census of human cancer genes","volume":"4","author":"PA Futreal","year":"2004","journal-title":"Nature Reviews Cancer"},{"issue":"3","key":"ref35","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/ng0398-287","article-title":"Peg3\/Pw1 is an imprinted gene involved in the TNF-NFkB signal transduction pathway","volume":"18","author":"F Relaix","year":"1998","journal-title":"Nat Genet"},{"issue":"22","key":"ref36","doi-asserted-by":"crossref","first-page":"12050","DOI":"10.1073\/pnas.97.22.12050","article-title":"Peg3\/Pw1 promotes p53-mediated apoptosis by inducing Bax translocation from cytosol to mitochondria","volume":"97","author":"Y Deng","year":"2000","journal-title":"Proc Natl Acad Sci"},{"issue":"16","key":"ref37","doi-asserted-by":"crossref","first-page":"6516","DOI":"10.1158\/0008-5472.CAN-09-4566","article-title":"KRAB zinc finger protein ZNF382 is a proapoptotic tumor suppressor that represses multiple oncogenes and is commonly silenced in multiple carcinomas","volume":"70","author":"Y Cheng","year":"2010","journal-title":"Cancer Research"},{"issue":"5","key":"ref38","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ncb1864","article-title":"KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis","volume":"11","author":"C Tian","year":"2009","journal-title":"Nature Cell Biology"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"17071","DOI":"10.1038\/cddiscovery.2017.71","article-title":"Zinc-finger proteins in health and disease","volume":"3","author":"M Cassandri","year":"2017","journal-title":"Cell Death Discovery"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s12929-016-0269-9","article-title":"Zinc finger proteins in cancer progression","volume":"23","author":"J Jen","year":"2016","journal-title":"Journal of Biomedical Science"},{"issue":"3","key":"ref41","doi-asserted-by":"crossref","first-page":"e1000869","DOI":"10.1371\/journal.pgen.1000869","article-title":"KRAB\u2013zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading","volume":"6","author":"AC Groner","year":"2010","journal-title":"PLOS Genetics"},{"issue":"6","key":"ref42","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.devcel.2016.02.024","article-title":"Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues","volume":"36","author":"G Ecco","year":"2016","journal-title":"Developmental Cell"},{"issue":"6097","key":"ref43","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1126\/science.1222077","article-title":"Landscape of somatic retrotransposition in human cancers","volume":"337","author":"E Lee","year":"2012","journal-title":"Science"},{"issue":"5","key":"ref44","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"MA DePristo","year":"2011","journal-title":"Nature Genetics"},{"issue":"1","key":"ref45","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.csda.2012.10.006","article-title":"On computing the distribution function for the Poisson binomial distribution","volume":"59","author":"Y Hong","year":"2013","journal-title":"Computational Statistics & Data Analysis"},{"issue":"1","key":"ref46","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1186\/s12859-016-1203-6","article-title":"NEAT: an efficient network enrichment analysis test","volume":"17","author":"M Signorelli","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"ref47","unstructured":"Storey JD, Bass A, Dabney A, Robinson D. qvalue: Q-value estimation for false discovery rate control; 2015. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/github.com\/jdstorey\/qvalue\" xlink:type=\"simple\">http:\/\/github.com\/jdstorey\/qvalue<\/ext-link>."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006290","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,7,11]],"date-time":"2018-07-11T00:00:00Z","timestamp":1531267200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006290","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,26]],"date-time":"2022-08-26T18:01:24Z","timestamp":1661536884000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006290"}},"subtitle":[],"editor":[{"given":"Marco","family":"Punta","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,28]]},"references-count":47,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2018,6,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006290","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006290","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,28]]}}}