{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:04:17Z","timestamp":1761919457803},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Animal models play a pivotal role in translation biomedical research. The scientific value of an animal model depends on how accurately it mimics the human disease. In principle, microarrays collect the necessary data to evaluate the transcriptomic fidelity of an animal model in terms of the similarity of expression with the human disease. However, statistical methods for this purpose are lacking.<\/jats:p>\n               <jats:p>Results: We develop the agreement of differential expression (AGDEX) procedure to measure and determine the statistical significance of the similarity of the results of two experiments that measure differential expression across two groups. AGDEX defines a metric of agreement and determines statistical significance by permutation of each experiment's group labels. Additionally, AGDEX performs a comprehensive permutation-based analysis of differential expression for each experiment, including gene-set analyses and meta-analytic integration of results across studies. As an example, we show how AGDEX was recently used to evaluate the similarity of the transcriptome of a novel model of the brain tumor ependymoma in mice to that of a subtype of the human disease. This result, combined with other observations, helped us to infer the cell of origin of this devastating human cancer.<\/jats:p>\n               <jats:p>Availability: An R package is currently available from www.stjuderesearch.org\/site\/depts\/biostats\/agdex and will shortly be available from www.bioconductor.org.<\/jats:p>\n               <jats:p>Contact: \u00a0stanley.pounds@stjude.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr362","type":"journal-article","created":{"date-parts":[[2011,6,23]],"date-time":"2011-06-23T00:58:29Z","timestamp":1308790709000},"page":"2098-2103","source":"Crossref","is-referenced-by-count":15,"title":["A procedure to statistically evaluate agreement of differential expression for cross-species genomics"],"prefix":"10.1093","volume":"27","author":[{"given":"Stan","family":"Pounds","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cuilan Lani","family":"Gao","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert A.","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen D.","family":"Wright","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen","family":"Poppleton","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Finkelstein","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah E. S.","family":"Leary","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard J.","family":"Gilbertson","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA, 2Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH, USA, 3Department of Oncology, 4Department of Developmental Neurobiology, 5Department of Information Sciences, St Jude Children's Research Hospital, Memphis, TN and 6Department of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,22]]},"reference":[{"key":"2023012511531803000_B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nrg1749","article-title":"Microarray data analysis: from disarray to consolidation and consensus","volume":"7","author":"Allison","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"2023012511531803000_B2","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","article-title":"Significance analysis of functional categories in gene expression studies: a structured permutation approach","volume":"21","author":"Barry","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012511531803000_B3","volume-title":"Advanced Calculus: a Course in Mathematical Analysis","author":"Fitzpatrick","year":"1996"},{"key":"2023012511531803000_B4","first-page":"365","article-title":"Randomization tests for small samples: an application for genetic expression data","volume":"52","author":"Gadbury","year":"2003","journal-title":"Appl. Stat."},{"key":"2023012511531803000_B5","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1038\/nature09587","article-title":"Subtypes of medulloblastoma have distinct developmental origins","volume":"468","author":"Gibson","year":"2010","journal-title":"Nature"},{"key":"2023012511531803000_B6","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","article-title":"Analyzing gene expression data in terms of gene sets: methodological issues","volume":"23","author":"Goeman","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012511531803000_B7","volume-title":"Permutation, Parametric, and Bootstrap Tests of Hypotheses","author":"Good","year":"2010","edition":"3rd"},{"key":"2023012511531803000_B8","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023012511531803000_B9","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/nature09173","article-title":"Cross-species genomics matches driver mutations and cell compartments to model ependymoma","volume":"466","author":"Johnson","year":"2010","journal-title":"Nature"},{"key":"2023012511531803000_B10","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/nature05690","article-title":"Genes regulating B cell development are mutated in acute lymphoid leukaemia","volume":"446","author":"Mullighan","year":"2007","journal-title":"Nature"},{"key":"2023012511531803000_B11","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1177\/117693510700300008","article-title":"Statistical issues and analysis of in vivo and in vitro genomic data in order to identify clinically relevant profiles","volume":"3","author":"Poisson","year":"2007","journal-title":"Cancer Informat."},{"key":"2023012511531803000_B12","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1089\/cmb.2005.12.482","article-title":"Statistical development and evaluation of gene expression data filters","volume":"12","author":"Pounds","year":"2005","journal-title":"J. Comput. Biol."},{"key":"2023012511531803000_B13","doi-asserted-by":"crossref","first-page":"4263","DOI":"10.1093\/bioinformatics\/bti699","article-title":"Sample size determination for the false discovery rate","volume":"21","author":"Pounds","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012511531803000_B14","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1093\/bib\/bbk002","article-title":"Estimation and control of multiple testing error rates for the analysis of microarray data","volume":"7","author":"Pounds","year":"2006","journal-title":"Brief. Bioinformatics"},{"key":"2023012511531803000_B15","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.brainres.2007.08.074","article-title":"Statistical analysis of data collected in retroviral clonal experiments in the developing retina","volume":"1192","author":"Pounds","year":"2008","journal-title":"Brain Res."},{"key":"2023012511531803000_B16","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1093\/bioinformatics\/btn624","article-title":"Reference alignment of SNP microarray signals for copy number analysis of tumors","volume":"25","author":"Pounds","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511531803000_B17","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1093\/bioinformatics\/btp357","article-title":"PROMISE: a tool to identify genomic variables with a specific biologically interesting pattern of associations with multiple endpoint variables","volume":"25","author":"Pounds","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511531803000_B18","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1504\/IJDMB.2011.039174","article-title":"Integrated analysis of pharmacokinetic, clinical, and SNP microarray data using projection onto the most interesting statistical evidence with adaptive permutation testing","volume":"5","author":"Pounds","year":"2011","journal-title":"Int. J. Data Min. Bioinformatics"},{"key":"2023012511531803000_B19","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1073\/pnas.0408105102","article-title":"Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI)","volume":"102","author":"Sandberg","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511531803000_B20","article-title":"The American Soldier","volume-title":"Adjustment during Army Life","author":"Stouffer","year":"1949"},{"key":"2023012511531803000_B21","doi-asserted-by":"crossref","first-page":"r124","DOI":"10.1186\/gb-2010-11-12-r124","article-title":"Large scale comparison of global gene expression patterns in human and mouse","volume":"11","author":"Zheng-Bradley","year":"2010","journal-title":"Genome Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/15\/2098\/48864949\/bioinformatics_27_15_2098.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/15\/2098\/48864949\/bioinformatics_27_15_2098.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:58:44Z","timestamp":1674647924000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/15\/2098\/404964"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,22]]},"references-count":21,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2011,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr362","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,8,1]]},"published":{"date-parts":[[2011,6,22]]}}}