{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T14:19:17Z","timestamp":1648649957766},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"S15","license":[{"start":{"date-parts":[[2012,9,1]],"date-time":"2012-09-01T00:00:00Z","timestamp":1346457600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,9]]},"DOI":"10.1186\/1471-2105-13-s15-s11","type":"journal-article","created":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T09:44:41Z","timestamp":1548150281000},"source":"Crossref","is-referenced-by-count":1,"title":["BirdsEyeView (BEV): graphical overviews of experimental data"],"prefix":"10.1186","volume":"13","author":[{"given":"Lifeng","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Berleant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diane","family":"Cook","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eve Syrkin","family":"Wurtele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,9,11]]},"reference":[{"key":"5354_CR1","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/1471-2229-8-99","volume":"8","author":"WI Mentzen","year":"2008","unstructured":"Mentzen WI, Wurtele ES: Regulon organization of Arabidopsis. BMC Plant Biology 2008, 8: 99. 10.1186\/1471-2229-8-99","journal-title":"BMC Plant Biology"},{"key":"5354_CR2","doi-asserted-by":"publisher","first-page":"D1002","DOI":"10.1093\/nar\/gkq1040","volume":"39","author":"H Parkinson","year":"2011","unstructured":"Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, et al.: ArrayExpress update--an archive of microarray and high-throughput sequencing based functional genomics experiments. Nucleic Acids Res 2011, 39: D1002. 10.1093\/nar\/gkq1040","journal-title":"Nucleic Acids Res"},{"key":"5354_CR3","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3389\/fpls.2012.00015","volume":"3","author":"SMM Quanbeck","year":"2012","unstructured":"Quanbeck SMM, Brachova L, Campbell AA, Guan X, Perera A, Seung KA, Rhee Y, Bais P, Dickerson J, Dixon P, et al.: Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of \"unknown function\". Front Plant Sci 2012, 3: 15.","journal-title":"Front Plant Sci"},{"key":"5354_CR4","volume-title":"Biotechnology for Medicinal Plants: Propagation and improvement","author":"MC Crispin","year":"2012","unstructured":"Crispin MC, Wurtele ES: Use of Metabolomics and Transcriptomics to Gain Insights into the Regulation and Biosynthesis of Medicinal Compounds: Hypericum as a Model. In Biotechnology for Medicinal Plants: Propagation and improvement. Edited by: Chandra C. Springer; 2012:in press. Chapter 18 Chapter 18"},{"issue":"7399","key":"5354_CR5","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/nature11009","volume":"485","author":"MN Ngaki","year":"2012","unstructured":"Ngaki MN, Louie GV, Manning G, Pojer F, Bowman ME, Li L, Elise Larsen E, Wurtele ES, Noel JP: Evolution of the Chalcone Isomerase Fold from Fatty Acid-Binding to Stereospecific Enzyme. Nature 2012, 485(7399):530\u2013533.","journal-title":"Nature"},{"key":"5354_CR6","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1186\/1471-2105-5-151","volume":"5","author":"IA Awad","year":"2004","unstructured":"Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G: Caryoscope: an open source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 2004, 5: 151. 10.1186\/1471-2105-5-151","journal-title":"BMC Bioinformatics"},{"key":"5354_CR7","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1186\/1471-2105-7-176","volume":"7","author":"TS Paul","year":"2006","unstructured":"Paul TS, David J, Richard B, Nitin SB: The Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 2006, 7: 176. 10.1186\/1471-2105-7-176","journal-title":"BMC Bioinformatics"},{"key":"5354_CR8","first-page":"453","volume":"3","author":"H Hochheiser","year":"2003","unstructured":"Hochheiser H, Baehrecke EH, Mount SM, Shneiderman B: Dynamic querying for pattern identification in microarray and genomic data. Proc IEEE Multimedia and Expo Int Conf 2003, 3: 453.","journal-title":"Proc IEEE Multimedia and Expo Int Conf"},{"key":"5354_CR9","first-page":"80","volume":"35","author":"J Seo","year":"2002","unstructured":"Seo J, Shneiderman B: Interactively exploring hierarchical clustering results. Computer 2002, 35: 80\u201386.","journal-title":"Computer"},{"key":"5354_CR10","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","volume":"34","author":"AI Saeed","year":"2003","unstructured":"Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al.: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34: 374\u2013378.","journal-title":"Biotechniques"},{"key":"5354_CR11","doi-asserted-by":"publisher","first-page":"3246","DOI":"10.1093\/bioinformatics\/bth349","volume":"20","author":"AJ Saldanha","year":"2004","unstructured":"Saldanha AJ: Java Treeview-extensible visualization of microarray data. Bioinformatics 2004, 20: 3246\u20133248. 10.1093\/bioinformatics\/bth349","journal-title":"Bioinformatics"},{"key":"5354_CR12","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/1471-2105-6-232","volume":"6","author":"S Ron","year":"2005","unstructured":"Ron S, Adi MK, Amos T, Chaim L, Israel S, Roded S, Yosef S, Ran E: EXPANDER-an integrative program suite for microarray data analysis. BMC Bioinformatics 2005, 6: 232. 10.1186\/1471-2105-6-232","journal-title":"BMC Bioinformatics"},{"key":"5354_CR13","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1186\/1471-2105-6-115","volume":"6","author":"MA Hibbs","year":"2005","unstructured":"Hibbs MA, Dirksen NC, Li K, Troyanskaya OG: Visualization methods for statistical analysis of microarray clusters. BMC Bioinformatics 2005, 6: 115. 10.1186\/1471-2105-6-115","journal-title":"BMC Bioinformatics"},{"key":"5354_CR14","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1093\/bioinformatics\/btl070","volume":"22","author":"J Dietzsch","year":"2006","unstructured":"Dietzsch J, Gehlenborg N, Nieselt K: Mayday - a microarray data analysis workbench. Bioinformatics 2006, 22: 1010\u20131012. 10.1093\/bioinformatics\/btl070","journal-title":"Bioinformatics"},{"key":"5354_CR15","doi-asserted-by":"publisher","first-page":"1779","DOI":"10.1093\/bioinformatics\/btq282","volume":"26","author":"F Aris","year":"2010","unstructured":"Aris F, Kenneth S, Zhou J, John W, Andrea C: geWorkbench: an open source platform for integrative genomics. Bioinformatics 2010, 26: 1779\u20131780. 10.1093\/bioinformatics\/btq282","journal-title":"Bioinformatics"},{"key":"5354_CR16","doi-asserted-by":"publisher","first-page":"D619","DOI":"10.1093\/nar\/gkn863","volume":"37","author":"L Matthews","year":"2009","unstructured":"Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, et al.: Reactome knowledgebase of biological pathways and processes. Nucleic Acids Res 2009, 37: D619\u2013622. 10.1093\/nar\/gkn863","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 4","key":"5354_CR17","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1753-6561-3-s4-s6","volume":"3","author":"A Jim\u00e9nez-Mar\u00edn","year":"2009","unstructured":"Jim\u00e9nez-Mar\u00edn A, Collado-Romero M, Ramirez-Boo M, Arce C, Garrido JJ: Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis. BMC Proceedings 2009, 3(Suppl 4):S6. 10.1186\/1753-6561-3-s4-s6","journal-title":"BMC Proceedings"},{"key":"5354_CR18","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1186\/1471-2105-12-176","volume":"12","author":"L Mario","year":"2011","unstructured":"Mario L, Peter DK: Web-based metabolic network visualization with a zooming user interface. BMC Bioinformatics 2011, 12: 176. 10.1186\/1471-2105-12-176","journal-title":"BMC Bioinformatics"},{"key":"5354_CR19","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1111\/j.1365-3040.2009.01978.x","volume":"32","author":"B Usadel","year":"2009","unstructured":"Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M: A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, maize. Plant Cell Environ 2009, 32: 1211\u20131229. 10.1111\/j.1365-3040.2009.01978.x","journal-title":"Plant Cell Environ"},{"key":"5354_CR20","doi-asserted-by":"publisher","first-page":"2366","DOI":"10.1038\/nprot.2007.324","volume":"2","author":"MS Cline","year":"2007","unstructured":"Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al.: Integration of biological networks and gene expression data using Cytoscape. Nature Protocols 2007, 2: 2366\u20132382. 10.1038\/nprot.2007.324","journal-title":"Nature Protocols"},{"key":"5354_CR21","first-page":"317","volume-title":"13th Int Conf Information Visualization","author":"R Bourqui","year":"2009","unstructured":"Bourqui R, Westenberg MA: Visualizing Temporal Dynamics at the Genomic and Metabolic Level. 13th Int Conf Information Visualization 2009, 317\u2013322."},{"key":"5354_CR22","doi-asserted-by":"publisher","first-page":"2112","DOI":"10.1093\/bioinformatics\/btn368","volume":"24","author":"K Robert","year":"2008","unstructured":"Robert K, Allan K, Michael C: VistaClara: an expression browser plug-in for Cytoscape. Bioinformatics 2008, 24: 2112\u20132114. 10.1093\/bioinformatics\/btn368","journal-title":"Bioinformatics"},{"key":"5354_CR23","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1186\/1471-2105-8-217","volume":"8","author":"N Salomonis","year":"2007","unstructured":"Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR: GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 2007, 8: 217. 10.1186\/1471-2105-8-217","journal-title":"BMC Bioinformatics"},{"key":"5354_CR24","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1186\/1471-2105-11-469","volume":"11","author":"M Jia","year":"2010","unstructured":"Jia M, Choi S-Y, Reiners D, Wurtele ES, Dickerson JA: MetNetGE: interactive views of biological networks and ontologies. BMC Bioinformatics 2010, 11: 469. 10.1186\/1471-2105-11-469","journal-title":"BMC Bioinformatics"},{"key":"5354_CR25","doi-asserted-by":"publisher","first-page":"D623","DOI":"10.1093\/nar\/gkm900","volume":"36","author":"R Caspi","year":"2008","unstructured":"Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases. Nucleic Acids Res 2008, 36: D623\u2013631.","journal-title":"Nucleic Acids Res"},{"key":"5354_CR26","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/978-1-4020-5608-6_10","volume-title":"Concepts in Plant Metabolomics","author":"ES Wurtele","year":"2007","unstructured":"Wurtele ES, Li L, Berleant D, Cook D, Dickerson JA, Ding J, Hofmann H, Lawrence M, Lee EK, Li J, et al.: MetNet: systems biology software for Arabidopsis . In Concepts in Plant Metabolomics. Edited by: Nikolau BJ, Wurtele ES. Springer; 2007:145\u2013158."},{"key":"5354_CR27","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1093\/bioinformatics\/btm057","volume":"23","author":"B Aaron","year":"2007","unstructured":"Aaron B, Jennifer LG, Robert EWH, Tamara M: Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 2007, 23: 1040\u20131042. 10.1093\/bioinformatics\/btm057","journal-title":"Bioinformatics"},{"key":"5354_CR28","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/1756-0500-2-124","volume":"2","author":"JP Goncalves","year":"2009","unstructured":"Goncalves JP, Madeira SC, Oliveira AL: BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data. BMC Res Notes 2 2009, 2: 124. 10.1186\/1756-0500-2-124","journal-title":"BMC Res Notes 2"},{"key":"5354_CR29","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1002\/cbdv.201100355","volume":"9","author":"YP Feng","year":"2012","unstructured":"Feng YP, Hurst J, Almeida-De-Macedo M, Chen X, Li L, Ransom N, Wurtele ES: Massive human co-expression-network and its medical applications. Chem Biodivers 2012, 9: 868\u2013887. 10.1002\/cbdv.201100355","journal-title":"Chem Biodivers"},{"key":"5354_CR30","unstructured":"Mittler R2009. [\n                    http:\/\/www.metnetdb.org\/bev\/newmittler3.gene.data.txt\n                    \n                  ]"},{"key":"5354_CR31","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1559\/152304003100010929","volume":"30","author":"CA Brewer","year":"2003","unstructured":"Brewer CA, Geoffrey WH, Mark AH: ColorBrewer in print: a catalog of color schemes for maps. Cartography and Geographic Information Science 2003, 30: 5\u201332. 10.1559\/152304003100010929","journal-title":"Cartography and Geographic Information Science"},{"key":"5354_CR32","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1145\/571647.571649","volume":"21","author":"BB Bederson","year":"2002","unstructured":"Bederson BB, Shneiderman B, Wattenberg M: Ordered and Quantum Treemaps: making effective use of 2D space to display hierarchies. ACM Transactions on Graphics (TOG) 2002, 21: 833\u2013854. 10.1145\/571647.571649","journal-title":"ACM Transactions on Graphics (TOG)"},{"key":"5354_CR33","unstructured":"Brandon L2009. [\n                    http:\/\/www.plexdb.org\/modules\/PD_browse\/experiment_browser.php?experiment=GM10\n                    \n                  ]"},{"key":"5354_CR34","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1007\/978-1-61779-361-5_19","volume":"804","author":"N Le Meur","year":"2012","unstructured":"Le Meur N, Gentleman R: Analyzing biological data using R: methods for graphs and networks. Methods Mol Biol 2012, 804: 343\u2013373. 10.1007\/978-1-61779-361-5_19","journal-title":"Methods Mol Biol"},{"key":"5354_CR35","first-page":"25","volume-title":"Journal of Statistical Software","author":"M Lawrence","year":"2008","unstructured":"Lawrence M, Cook D, Lee EK, Babka H, Wurtele ES: 2008: Explorase: Multivariate Exploratory Analysis and Visualization. Journal of Statistical Software 2008, 25."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S15-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-S15-S11\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S15-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T10:08:08Z","timestamp":1548151688000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S15-S11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9]]},"references-count":35,"journal-issue":{"issue":"S15","published-print":{"date-parts":[[2012,9]]}},"alternative-id":["5354"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s15-s11","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,9]]},"article-number":"S11"}}