{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T15:10:07Z","timestamp":1717945807631},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,6,1]],"date-time":"2015-06-01T00:00:00Z","timestamp":1433116800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BioData Mining"],"published-print":{"date-parts":[[2015,6]]},"DOI":"10.1186\/s13040-015-0050-8","type":"journal-article","created":{"date-parts":[[2015,6,16]],"date-time":"2015-06-16T14:11:43Z","timestamp":1434463903000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study"],"prefix":"10.1186","volume":"8","author":[{"given":"Jiang","family":"Gui","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Casey S.","family":"Greene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Con","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason H.","family":"Moore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carol","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,6,17]]},"reference":[{"issue":"9","key":"50_CR1","doi-asserted-by":"publisher","first-page":"1509","DOI":"10.1101\/gr.079558.108","volume":"18","author":"JC Marioni","year":"2008","unstructured":"Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18(9):1509\u201317. PMCID: PMC2527709.","journal-title":"Genome Res"},{"key":"50_CR2","unstructured":"Bonferroni CE. Il calcolo delle assicurazioni su gruppi di teste. Tipografia del Senato; 1935."},{"issue":"1","key":"50_CR3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B Met. 1995;57(1):289\u2013300.","journal-title":"J Roy Stat Soc B Met"},{"key":"50_CR4","doi-asserted-by":"crossref","unstructured":"Smyth GK. Limma: Linear models for microarray data. In: Bioinformatics and computational biology solutions using R and Bioconductor. Springer; 2005. p. 397\u2013420.","DOI":"10.1007\/0-387-29362-0_23"},{"issue":"5","key":"50_CR5","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511\u20135.","journal-title":"Nat Biotechnol"},{"issue":"10","key":"50_CR6","doi-asserted-by":"publisher","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","volume":"11","author":"S Anders","year":"2010","unstructured":"Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.","journal-title":"Genome Biol"},{"issue":"1","key":"50_CR7","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1756-0381-5-4","volume":"5","author":"J Gui","year":"2012","unstructured":"Gui J, Tosteson TD, Borsuk M. Weighted multiple testing procedures for genomic studies. BioData Min. 2012;5(1):4. PMCID: PMC3458887.","journal-title":"BioData Min"},{"issue":"3","key":"50_CR8","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1093\/biomet\/93.3.509","volume":"93","author":"CR Genovese","year":"2006","unstructured":"Genovese CR, Roeder K, Wasserman L. False discovery control with p-value weighting. Biometrika. 2006;93(3):509\u201324.","journal-title":"Biometrika"},{"issue":"Web Server issu","key":"50_CR9","doi-asserted-by":"publisher","first-page":"W484","DOI":"10.1093\/nar\/gks458","volume":"40","author":"AK Wong","year":"2012","unstructured":"Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. IMP: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 2012;40(Web Server issue):W484\u201390. PMCID: PMC3394282.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"50_CR10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002957","volume":"9","author":"CY Park","year":"2013","unstructured":"Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, et al. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS computational biology. 2013;9(3), e1002957.","journal-title":"PLoS computational biology"},{"issue":"6","key":"50_CR11","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1101\/gr.082214.108","volume":"19","author":"C Huttenhower","year":"2009","unstructured":"Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, et al. Exploring the human genome with functional maps. Genome Res. 2009;19(6):1093\u2013106. PMCID: PMC2694471.","journal-title":"Genome Res"},{"issue":"9","key":"50_CR12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0023637","volume":"6","author":"RL Young","year":"2011","unstructured":"Young RL, Malcolm KC, Kret JE, Caceres SM, Poch KR, Nichols DP, et al. Neutrophil extracellular trap (NET)-mediated killing of pseudomonas aeruginosa: Evidence of acquired resistance within the CF airway, independent of CFTR. PLoS One. 2011;6(9), e23637.","journal-title":"PLoS One"},{"issue":"21","key":"50_CR13","doi-asserted-by":"publisher","first-page":"17130","DOI":"10.1074\/jbc.M111.338855","volume":"287","author":"JM Bomberger","year":"2012","unstructured":"Bomberger JM, Coutermarsh BA, Barnaby RL, Stanton BA. Arsenic promotes ubiquitinylation and lysosomal degradation of cystic fibrosis transmembrane conductance regulator (CFTR) chloride channels in human airway epithelial cells. J Biol Chem. 2012;287(21):17130\u20139. PMCID: PMC3366821.","journal-title":"J Biol Chem"},{"issue":"2","key":"50_CR14","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/j.aquatox.2010.02.001","volume":"98","author":"JR Shaw","year":"2010","unstructured":"Shaw JR, Bomberger JM, VanderHeide J, LaCasse T, Stanton S, Coutermarsh B, et al. Arsenic inhibits SGK1 activation of CFTR cl< sup>\u2212<\/sup> channels in the gill of killifish,< i> fundulus heteroclitus<\/i> Aquatic toxicology. 2010;98(2):157\u201364.","journal-title":"Aquatic toxicology"},{"issue":"1","key":"50_CR15","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1093\/toxsci\/kfm072","volume":"98","author":"AS Nayak","year":"2007","unstructured":"Nayak AS, Lage CR, Kim CH. Effects of low concentrations of arsenic on the innate immune system of the zebrafish (danio rerio). Toxicol Sci. 2007;98(1):118\u201324.","journal-title":"Toxicol Sci"},{"issue":"3","key":"50_CR16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000322","volume":"5","author":"MA Hibbs","year":"2009","unstructured":"Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, et al. Directing experimental biology: A case study in mitochondrial biogenesis. PLoS computational biology. 2009;5(3), e1000322.","journal-title":"PLoS computational biology"},{"issue":"9","key":"50_CR17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000165","volume":"4","author":"Y Guan","year":"2008","unstructured":"Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A genomewide functional network for the laboratory mouse. PLoS computational biology. 2008;4(9), e1000165.","journal-title":"PLoS computational biology"},{"issue":"6","key":"50_CR18","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1093\/icb\/icl048","volume":"46","author":"CR Lage","year":"2006","unstructured":"Lage CR, Nayak A, Kim CH. Arsenic ecotoxicology and innate immunity. Integr Comp Biol. 2006;46(6):1040\u201354.","journal-title":"Integr Comp Biol"},{"issue":"5","key":"50_CR19","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1007\/s10126-004-4109-7","volume":"7","author":"AC Hermann","year":"2005","unstructured":"Hermann AC, Kim CH. Effects of arsenic on zebrafish innate immune system. Marine Biotechnology. 2005;7(5):494\u2013505.","journal-title":"Marine Biotechnology"},{"issue":"11","key":"50_CR20","doi-asserted-by":"publisher","first-page":"4542","DOI":"10.1128\/IAI.00302-10","volume":"78","author":"RT Phennicie","year":"2010","unstructured":"Phennicie RT, Sullivan MJ, Singer JT, Yoder JA, Kim CH. Specific resistance to pseudomonas aeruginosa infection in zebrafish is mediated by the cystic fibrosis transmembrane conductance regulator. Infect Immun. 2010;78(11):4542\u201350. PMCID: PMC2976322.","journal-title":"Infect Immun"},{"issue":"16","key":"50_CR21","doi-asserted-by":"publisher","first-page":"8181","DOI":"10.1128\/JVI.00521-11","volume":"85","author":"OJ Hamming","year":"2011","unstructured":"Hamming OJ, Lutfalla G, Levraud JP, Hartmann R. Crystal structure of zebrafish interferons I and II reveals conservation of type I interferon structure in vertebrates. J Virol. 2011;85(16):8181\u20137. PMCID: PMC3147990.","journal-title":"J Virol"},{"issue":"4","key":"50_CR22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002641","volume":"8","author":"LM Bradley","year":"2012","unstructured":"Bradley LM, Douglass MF, Chatterjee D, Akira S, Baaten BJ. Matrix metalloprotease 9 mediates neutrophil migration into the airways in response to influenza virus-induced toll-like receptor signaling. PLoS pathogens. 2012;8(4), e1002641.","journal-title":"PLoS pathogens"},{"issue":"9","key":"50_CR23","doi-asserted-by":"publisher","first-page":"1765","DOI":"10.1038\/nprot.2013.099","volume":"8","author":"S Anders","year":"2013","unstructured":"Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, et al. Count-based differential expression analysis of RNA sequencing data using R and bioconductor. Nature protocols. 2013;8(9):1765\u201386.","journal-title":"Nature protocols"},{"issue":"4","key":"50_CR24","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1214\/09-STS289","volume":"24","author":"K Roeder","year":"2009","unstructured":"Roeder K, Wasserman L. Genome-wide significance levels and weighted hypothesis testing. Stat Sci. 2009;24(4):398\u2013413. PMCID: PMC2920568.","journal-title":"Stat Sci"}],"container-title":["BioData Mining"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13040-015-0050-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13040-015-0050-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13040-015-0050-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13040-015-0050-8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T14:55:40Z","timestamp":1717944940000},"score":1,"resource":{"primary":{"URL":"https:\/\/biodatamining.biomedcentral.com\/articles\/10.1186\/s13040-015-0050-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6]]},"references-count":24,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,6]]}},"alternative-id":["50"],"URL":"https:\/\/doi.org\/10.1186\/s13040-015-0050-8","relation":{},"ISSN":["1756-0381"],"issn-type":[{"value":"1756-0381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,6]]},"assertion":[{"value":"3 December 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 June 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 June 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"17"}}