{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T14:17:01Z","timestamp":1793197021570,"version":"4.5.0"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2012,7,17]],"date-time":"2012-07-17T00:00:00Z","timestamp":1342483200000},"content-version":"unspecified","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.0041169","type":"journal-article","created":{"date-parts":[[2012,7,19]],"date-time":"2012-07-19T07:43:45Z","timestamp":1342683825000},"page":"e41169","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":105,"title":["Global Transcriptome Analysis in Influenza-Infected Mouse Lungs Reveals the Kinetics of Innate and Adaptive Host Immune Responses"],"prefix":"10.1371","volume":"7","author":[{"given":"Claudia","family":"Pommerenke","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"Wilk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barkha","family":"Srivastava","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annika","family":"Schulze","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Novoselova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Geffers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Klaus","family":"Schughart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2012,7,17]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1353\/bhm.2002.0022","article-title":"Updating the accounts: global mortality of the 1918\u20131920 \u201cSpanish\u201d influenza pandemic.","volume":"76","author":"NP Johnson","year":"2002","journal-title":"Bull Hist Med"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"S73","DOI":"10.1086\/507550","article-title":"Seasonal and pandemic influenza preparedness: science and countermeasures.","volume":"194","author":"AS Fauci","year":"2006","journal-title":"J Infect Dis"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1111\/j.1600-065X.2008.00737.x","article-title":"Innate immunity to virus infection.","volume":"227","author":"O Takeuchi","year":"2009","journal-title":"Immunol Rev"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/j.immuni.2007.08.012","article-title":"Innate recognition of viruses.","volume":"27","author":"A Pichlmair","year":"2007","journal-title":"Immunity"},{"key":"ref5","first-page":"73","article-title":"The interferon response circuit in antiviral host defense.","volume":"71","author":"O Haller","year":"2009","journal-title":"Verh K Acad Geneeskd Belg"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/j.coi.2007.08.004","article-title":"Beyond inflammation: airway epithelial cells are at the interface of innate and adaptive immunity.","volume":"19","author":"A Kato","year":"2007","journal-title":"Curr Opin Immunol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1146\/annurev.immunol.021908.132625","article-title":"Immunity to respiratory viruses.","volume":"27","author":"JE Kohlmeier","year":"2009","journal-title":"Annu Rev Immunol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"S32","DOI":"10.1016\/S0264-410X(00)00275-9","article-title":"Inflammatory responses in influenza A virus infection.","volume":"19","author":"I Julkunen","year":"2000","journal-title":"Vaccine"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/S1359-6101(00)00026-5","article-title":"Molecular pathogenesis of influenza A virus infection and virus-induced regulation of cytokine gene expression.","volume":"12","author":"I Julkunen","year":"2001","journal-title":"Cytokine Growth Factor Rev"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1189\/jlb.0509368","article-title":"Innate immune control and regulation of influenza virus infections.","volume":"86","author":"J McGill","year":"2009","journal-title":"J Leukoc Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/ni1322","article-title":"Lethal influenza infection in the absence of the natural killer cell receptor gene Ncr1.","volume":"7","author":"R Gazit","year":"2006","journal-title":"Nat Immunol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"48","DOI":"10.3201\/eid1201.051237","article-title":"Cell-mediated protection in influenza infection.","volume":"12","author":"PG Thomas","year":"2006","journal-title":"Emerg Infect Dis"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1111\/j.1600-065X.1997.tb01010.x","article-title":"Effector CD4+ and CD8+ T-cell mechanisms in the control of respiratory virus infections.","volume":"159","author":"PC Doherty","year":"1997","journal-title":"Immunol Rev"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e4857","DOI":"10.1371\/journal.pone.0004857","article-title":"Host genetic background strongly influences the response to influenza a virus infections.","volume":"4","author":"B Srivastava","year":"2009","journal-title":"PLoS ONE"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/1465-9921-12-61","article-title":"Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures.","volume":"12","author":"R Alberts","year":"2011","journal-title":"Respir Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1038\/nri2832","article-title":"New insights into the development of lymphoid tissues.","volume":"10","author":"SA van de Pavert","year":"2010","journal-title":"Nat Rev Immunol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/0092-8674(92)90030-G","article-title":"RAG-1-deficient mice have no mature B and T lymphocytes.","volume":"68","author":"P Mombaerts","year":"1992","journal-title":"Cell"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/0092-8674(92)90029-C","article-title":"RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement.","volume":"68","author":"Y Shinkai","year":"1992","journal-title":"Cell"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1101\/gad.8.9.1030","article-title":"Functional immunoglobulin transgenes guide ordered B-cell differentiation in Rag-1-deficient mice.","volume":"8","author":"E Spanopoulou","year":"1994","journal-title":"Genes Dev"},{"key":"ref20","article-title":"Immunobiology: The Immune System in Health and Disease: Garland Science.","author":"CA Janeway","year":"2001"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"11308","DOI":"10.1128\/JVI.00691-08","article-title":"Gene expression analysis of host innate immune responses during Lethal H5N1 infection in ferrets.","volume":"82","author":"CM Cameron","year":"2008","journal-title":"J Virol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/j.1601-183X.2007.00335.x","article-title":"Gene expression in lung and basal forebrain during influenza infection in mice.","volume":"7","author":"M Ding","year":"2008","journal-title":"Genes Brain Behav"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/nature05181","article-title":"Genomic Analysis of Increased Host Immune and Cell Death Responses Induced by 1918 Influenza Virus.","volume":"443","author":"JC Kash","year":"2006","journal-title":"Nature"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nature05495","article-title":"Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus.","volume":"445","author":"D Kobasa","year":"2007","journal-title":"Nature"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1111\/j.1365-2567.2006.02514.x","article-title":"Comparative transcriptional profiling of the lung reveals shared and distinct features of Streptococcus pneumoniae and influenza A virus infection.","volume":"120","author":"S Rosseau","year":"2007","journal-title":"Immunology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"6","DOI":"10.7883\/yoken.JJID.2009.6","article-title":"Expression and DNA microarray analysis of a platelet activating factor-related molecule in severe pneumonia in mice due to influenza virus and bacterial co-infection.","volume":"62","author":"M Seki","year":"2009","journal-title":"Jpn J Infect Dis"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"10417","DOI":"10.1128\/JVI.00514-09","article-title":"Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice.","volume":"83","author":"AC Boon","year":"2009","journal-title":"J Virol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.micinf.2010.01.008","article-title":"Gene expression changes in the host response between resistant and susceptible inbred mouse strains after influenza A infection.","volume":"12","author":"R Alberts","year":"2010","journal-title":"Microbes Infect"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.chom.2009.07.006","article-title":"Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans.","volume":"6","year":"2009","journal-title":"Cell Host Microbe"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"9499","DOI":"10.1128\/JVI.78.17.9499-9511.2004","article-title":"Global host immune response: pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus.","volume":"78","author":"JC Kash","year":"2004","journal-title":"J Virol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e1000604","DOI":"10.1371\/journal.ppat.1000604","article-title":"Lethal influenza virus infection in macaques is associated with early dysregulation of inflammatory related genes.","volume":"5","author":"C Cilloniz","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1016\/j.micinf.2006.04.018","article-title":"Signature patterns revealed by microarray analyses of mice infected with influenza virus A and Streptococcus pneumoniae.","volume":"8","author":"H Zhang","year":"2006","journal-title":"Microbes Infect"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"10420","DOI":"10.1128\/JVI.78.19.10420-10432.2004","article-title":"Integration of clinical data, pathology, and cDNA microarrays in influenza virus-infected pigtailed macaques (Macaca nemestrina).","volume":"78","author":"CR Baskin","year":"2004","journal-title":"J Virol"},{"key":"ref34","article-title":"H5N1 Virus Activates Signaling Pathways in Human Endothelial Cells Resulting in a Specific Imbalanced Inflammatory Response.","author":"D Viemann","year":"2010"},{"key":"ref35","doi-asserted-by":"crossref","DOI":"10.1165\/rcmb.2010-0108OC","article-title":"Innate Immune Response to Influenza A Virus in Differentiated Human Alveolar Type II cells.","author":"J Wang","year":"2011"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/1465-9921-11-147","article-title":"Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses in primary human type I-like alveolar epithelial cells in vitro.","volume":"11","author":"SM Lee","year":"2010","journal-title":"Respir Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1186\/1743-422X-7-219","article-title":"Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: a comparative analysis between highly pathogenic and modified H5N1 viruses.","volume":"7","author":"AK Chakrabarti","year":"2010","journal-title":"Virol J"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1534\/g3.111.001800","article-title":"Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice.","volume":"2","author":"D Bottomly","year":"2012","journal-title":"G3 (Bethesda)"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.virol.2010.12.047","article-title":"Pathogenicity of different PR8 influenza A virus variants in mice is determined by both viral and host factors.","volume":"412","author":"P Blazejewska","year":"2011","journal-title":"Virology"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1186\/1465-9921-10-112","article-title":"Impaired immune responses in the lungs of aged mice following influenza infection.","volume":"10","author":"FR Toapanta","year":"2009","journal-title":"Respir Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1038\/nm1091","article-title":"Role of inducible bronchus associated lymphoid tissue (iBALT) in respiratory immunity.","volume":"10","author":"JE Moyron-Quiroz","year":"2004","journal-title":"Nat Med"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1126\/science.1112422","article-title":"Recognition of host immune activation by Pseudomonas aeruginosa.","volume":"309","author":"L Wu","year":"2005","journal-title":"Science"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/2043-9113-1-27","article-title":"Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection.","volume":"1","author":"K Dimitrakopoulou","year":"2011","journal-title":"J Clin Bioinforma"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/1743-422X-7-172","article-title":"Sustained viral load and late death in Rag2<sup>\u2212\/\u2212<\/sup> mice after influenza A virus infection.","volume":"7","author":"H Wu","year":"2010","journal-title":"Virol J"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"2700","DOI":"10.1093\/bioinformatics\/btm412","article-title":"A comparison of background correction methods for two-colour microarrays.","volume":"23","author":"ME Ritchie","year":"2007","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1186\/1471-2164-10-439","article-title":"Relative power and sample size analysis on gene expression profiling data.","volume":"10","author":"M van Iterson","year":"2009","journal-title":"BMC Genomics"},{"key":"ref47","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 differentially regulated genes in replicated microarray experiments.","volume":"573","author":"R Breitling","year":"2004","journal-title":"FEBS Lett"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1109\/TPAMI.2004.1265860","article-title":"A Similarity-Based Robust Clustering Method.","volume":"26","author":"M-J Yang","year":"2004","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"ref49","first-page":"150","article-title":"Mining gene expression datasets using density-based clustering.","author":"S Chung","year":"2004"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/btl567","article-title":"Using GOstats to test gene lists for GO term association.","volume":"23","author":"S Falcon","year":"2007","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bioinformatics\/btn577","article-title":"A novel signaling pathway impact analysis.","volume":"25","author":"AL Tarca","year":"2009","journal-title":"Bioinformatics"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0041169","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,27]],"date-time":"2024-04-27T06:54:25Z","timestamp":1714200865000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0041169"}},"subtitle":[],"editor":[{"given":"George","family":"Kassiotis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2012,7,17]]},"references-count":51,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2012,7,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0041169","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,7,17]]}}}