{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,6]],"date-time":"2022-04-06T02:21:52Z","timestamp":1649211712526},"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2015,3,20]],"date-time":"2015-03-20T00:00:00Z","timestamp":1426809600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0119631","type":"journal-article","created":{"date-parts":[[2015,3,20]],"date-time":"2015-03-20T19:37:11Z","timestamp":1426880231000},"page":"e0119631","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets"],"prefix":"10.1371","volume":"10","author":[{"given":"Hugo P.","family":"Bastos","sequence":"first","affiliation":[]},{"given":"Lisete","family":"Sousa","sequence":"additional","affiliation":[]},{"given":"Luka A.","family":"Clarke","sequence":"additional","affiliation":[]},{"given":"Francisco M.","family":"Couto","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2015,3,20]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1093\/bib\/bbr002","article-title":"The what, where, how and why of gene ontology\u2014a primer for bioinformaticians","volume":"12","author":"L du Plessis","year":"2011","journal-title":"Briefings in Bioinformatics"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/nmeth.2340","article-title":"A large-scale evaluation of computational protein function prediction","volume":"10","author":"P Radivojac","year":"2013","journal-title":"Nat Meth"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.sbi.2005.05.010","article-title":"Automatic annotation of protein function","volume":"15","author":"A Valencia","year":"2005","journal-title":"Current Opinion in Structural Biology"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. the gene ontology consortium.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"DW Huang","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/1471-2105-6-189","article-title":"Gobar: A gene ontology based analysis and visualization tool for gene sets","volume":"6","author":"J Lee","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-7-443","article-title":"Golem: an interactive graph-based gene-ontology navigation and analysis tool","volume":"7","author":"R Sealfon","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/1471-2105-10-48","article-title":"Gorilla: a tool for discovery and visualization of enriched go terms in ranked gene lists","volume":"10","author":"E Eden","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref9","article-title":"Exploiting statistical methodologies and controlled vocabularies for prioritized functional analysis of genomic experiments: The stranger web application","volume":"5","author":"AA Chatziioannou","year":"2011","journal-title":"Frontiers in Neuroscience"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e78383","DOI":"10.1371\/journal.pone.0078383","article-title":"Panada: Protein association network annotation, determination and analysis","volume":"8","author":"AJM Martin","year":"2013","journal-title":"PLoS ONE"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: Current approaches and outstanding challenges","volume":"8","author":"P Khatri","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref12","first-page":"1203","article-title":"An open graph visualization system and its applications to software engineering","volume":"30","author":"ER Gansner","year":"2000","journal-title":"Software: Practice and Experience"},{"key":"ref13","first-page":"483","article-title":"Graphviz - Open Source Graph Drawing Tools","author":"J Ellson","year":"2001","journal-title":"Graph Drawing"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1093\/nar\/gkn803","article-title":"The goa database in 2009 - an integrated gene ontology annotation resource","volume":"37","author":"D Barrell","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref15","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2013.00201","article-title":"Annotation extension through protein family annotation coherence metrics","volume":"4","author":"HP Bastos","year":"2013","journal-title":"Frontiers in Genetics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating go graph structure","volume":"22","author":"A Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"ref17","article-title":"Chapman &amp; Hall\/CRC Mathematical &amp; Computational Biology","author":"P Robinson","year":"2011"},{"key":"ref18","first-page":"448","article-title":"Using information content to evaluate semantic similarity in a taxonomy","author":"P Resnik","year":"1995","journal-title":"In Proceedings of the 14th International Joint Conference on Artificial Intelligence"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-9-S5-S4","article-title":"Metrics for go based protein semantic similarity: a systematic evaluation","volume":"9","author":"C Pesquita","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gkn663","article-title":"The carbohydrate-active enzymes database (cazy): an expert resource for glycogenomics","volume":"37","author":"BL Cantarel","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1042\/BJ20101185","article-title":"A hierarchical classification of polysaccharide lyases for glycogenomics","volume":"432","author":"V Lombard","year":"2010","journal-title":"Biochemical Journal"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1093\/nar\/gkn1005","article-title":"Up-to-date catalogues of yeast protein complexes","volume":"37","author":"S Pu","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1002\/pmic.200600636","article-title":"Identifying functional modules in the physical interactome of saccharomyces cerevisiae","volume":"7","author":"S Pu","year":"2007","journal-title":"PROTEOMICS"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"D343","DOI":"10.1093\/nar\/gkr987","article-title":"Merops: the database of proteolytic enzymes, their substrates and inhibitors","volume":"40","author":"ND Rawlings","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1465-9921-14-38","article-title":"Changes in transcriptome of native nasal epithelium expressing f508del-cftr and intersecting data from comparable studies","volume":"14","author":"LA Clarke","year":"2013","journal-title":"Respiratory Research"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.febslet.2004.07.055","article-title":"Rank products: a simple, yet powerful, new method to detect di erentially regulated genes in replicated microarray experiments","volume":"573","author":"R Breitling","year":"2004","journal-title":"FEBS letters"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1378\/chest.13-2736","article-title":"Emerging role of micrornas and long noncoding rnas in respiratory disease","volume":"146","author":"R Booton","year":"2014","journal-title":"Chest"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1007\/s10495-013-0874-y","article-title":"Apoptotic process in cystic fibrosis cells","volume":"18","author":"R Soleti","year":"2013","journal-title":"Apoptosis"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1002\/path.2118","article-title":"Human airway surface epithelial regeneration is delayed and abnormal in cystic fibrosis","volume":"211","author":"R Hajj","year":"2007","journal-title":"The Journal of Pathology"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0119631","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,24]],"date-time":"2018-10-24T01:58:01Z","timestamp":1540346281000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0119631"}},"subtitle":[],"editor":[{"given":"Silvio C E","family":"Tosatto","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2015,3,20]]},"references-count":29,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2015,3,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0119631","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,20]]}}}