{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T10:29:58Z","timestamp":1721644198080},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2631,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Background: Recent improvements in DNA microarray techniques have made a large variety of gene expression data available in public databases. This data can be used to evaluate the strength of gene coexpression by calculating the correlation of expression patterns among different genes between many experiments. However, gene expression levels differ significantly across various tissues in higher organisms, as well as in different cellular location in eukaryotes in different cell state. Thus the usual correlation measure can only evaluate the difference of tissues or cellular localizations, and cannot adequately elucidate the functional relationship from the coexpression of genes.<\/jats:p>\n               <jats:p>Method: We propose a new measure of coexpression by expanding the generally used correlation into a multidimensional one. We used principal component analyses to identify the major factors of gene expression correlation, and then re-calculate the correlation by subtracting the major components in order to remove biases cased by a few experiments. The repeated subtractions of the major components yielded a set of correlation values for each pair of genes. We observed the correlation changes when the first ten principal components were subtracted step-by-step in large-scale Arabidopsis expression data.<\/jats:p>\n               <jats:p>Results: We found two extreme patterns of correlation changes, corresponding to stable and fragile coexpression. Our new indexes provided a good means to determine the functional relationships of the genes, by examining a few examples, and higher performance of Gene Ontology term prediction by using the support vector machine and the multidimensional correlation.<\/jats:p>\n               <jats:p>Availability: The results are available from the expression detail pages in ATTED-II (http:\/\/atted.jp).<\/jats:p>\n               <jats:p>Contact: \u00a0kinosita@hgc.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp442","type":"journal-article","created":{"date-parts":[[2009,7,21]],"date-time":"2009-07-21T00:58:23Z","timestamp":1248137903000},"page":"2677-2684","source":"Crossref","is-referenced-by-count":20,"title":["Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis"],"prefix":"10.1093","volume":"25","author":[{"given":"Kengo","family":"Kinoshita","sequence":"first","affiliation":[{"name":"1 Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639 and 2 Bioinformatics Research and Development, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan"},{"name":"1 Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639 and 2 Bioinformatics Research and Development, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan"}]},{"given":"Takeshi","family":"Obayashi","sequence":"additional","affiliation":[{"name":"1 Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639 and 2 Bioinformatics Research and Development, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan"}]}],"member":"286","published-online":{"date-parts":[[2009,7,20]]},"reference":[{"key":"2023013112130572000_B1","doi-asserted-by":"crossref","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","article-title":"Singular value decomposition for genome-wide expression data processing and modeling","volume":"97","author":"Alter","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112130572000_B2","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/pcp\/pcm013","article-title":"Approaches for extracting practical information from gene co-expression networks in plant biology","volume":"48","author":"Aoki","year":"2007","journal-title":"Plant Cell Physiol."},{"key":"2023013112130572000_B3","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":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023013112130572000_B4","doi-asserted-by":"crossref","first-page":"D760","DOI":"10.1093\/nar\/gkl887","article-title":"NCBI GEO: mining tens of millions of expression profiles\u2014database and tools update","volume":"35","author":"Barrett","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B5","doi-asserted-by":"crossref","first-page":"4164","DOI":"10.1073\/pnas.0308531101","article-title":"Metagenes and molecular pattern discovery using matrix factorization","volume":"101","author":"Brunet","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112130572000_B6","doi-asserted-by":"crossref","first-page":"D841","DOI":"10.1093\/nar\/gkl835","article-title":"PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses","volume":"35","author":"Bulow","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B7","doi-asserted-by":"crossref","first-page":"D575","DOI":"10.1093\/nar\/gkh133","article-title":"NASCArrays: a repository for microarray data generated by NASC's transcriptomics service","volume":"32","author":"Craigon","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B8","doi-asserted-by":"crossref","first-page":"D999","DOI":"10.1093\/nar\/gkm844","article-title":"AtPID: Arabidopsis thaliana protein interactome database\u2014an integrative platform for plant systems biology","volume":"36","author":"Cui","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B9","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"Eisen","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112130572000_B10","first-page":"1889","article-title":"Working set selection using second order information for training SVM","volume":"6","author":"Fan","year":"2005","journal-title":"J. Machine Learn. Res."},{"key":"2023013112130572000_B11","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1093\/dnares\/dsn025","article-title":"SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana","volume":"15","author":"Fukushima","year":"2008","journal-title":"DNA Res."},{"key":"2023013112130572000_B12","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1093\/bioinformatics\/btm403","article-title":"Exploring the functional landscape of gene expression: directed search of large microarray compendia","volume":"23","author":"Hibbs","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112130572000_B13","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","article-title":"Functional discovery via a compendium of expression profiles","volume":"102","author":"Hughes","year":"2000","journal-title":"Cell"},{"key":"2023013112130572000_B14","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/j.crvi.2003.09.034","article-title":"CIBEX: center for information biology gene expression database","volume":"326","author":"Ikeo","year":"2003","journal-title":"C R Biol."},{"key":"2023013112130572000_B15","doi-asserted-by":"crossref","first-page":"W460","DOI":"10.1093\/nar\/gkm363","article-title":"PrDOS: prediction of disordered protein regions from amino acid sequence","volume":"35","author":"Ishida","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B16","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1104\/pp.107.105866","article-title":"Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis","volume":"145","author":"Ishihara","year":"2007","journal-title":"Plant Physiol."},{"key":"2023013112130572000_B17","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"Kanehisa","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B18","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1093\/bioinformatics\/bti096","article-title":"Finding regulatory modules through large-scale gene-expression data analysis","volume":"21","author":"Kloster","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013112130572000_B19","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1101\/gr.1910904","article-title":"Coexpression analysis of human genes across many microarray data sets","volume":"14","author":"Lee","year":"2004","journal-title":"Genome Res."},{"key":"2023013112130572000_B20","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1126\/science.1099511","article-title":"A probabilistic functional network of yeast genes","volume":"306","author":"Lee","year":"2004","journal-title":"Science"},{"key":"2023013112130572000_B21","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/ng.2007.70","article-title":"A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans","volume":"40","author":"Lee","year":"2008","journal-title":"Nat. Genet."},{"key":"2023013112130572000_B22","doi-asserted-by":"crossref","first-page":"1724","DOI":"10.1371\/journal.pgen.0030161","article-title":"Capturing heterogeneity in gene expression studies by surrogate variable analysis","volume":"3","author":"Leek","year":"2007","journal-title":"PLoS Genet."},{"key":"2023013112130572000_B23","doi-asserted-by":"crossref","first-page":"W504","DOI":"10.1093\/nar\/gkl204","article-title":"Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis","volume":"34","author":"Manfield","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B24","doi-asserted-by":"crossref","first-page":"D863","DOI":"10.1093\/nar\/gkl783","article-title":"ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis","volume":"35","author":"Obayashi","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B25","doi-asserted-by":"crossref","first-page":"D77","DOI":"10.1093\/nar\/gkm840","article-title":"COXPRESdb: a database of coexpressed gene networks in mammals","volume":"36","author":"Obayashi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B26","doi-asserted-by":"crossref","first-page":"D987","DOI":"10.1093\/nar\/gkn807","article-title":"ATTED-II provides coexpressed gene networks for Arabidopsis","volume":"37","author":"Obayashi","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B27","doi-asserted-by":"crossref","first-page":"D747","DOI":"10.1093\/nar\/gkl995","article-title":"ArrayExpress\u2014a public database of microarray experiments and gene expression profiles","volume":"35","author":"Parkinson","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B28","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/S0014-5793(02)03634-7","article-title":"The HCF136 protein is essential for assembly of the photosystem II reaction center in Arabidopsis thaliana","volume":"532","author":"Plucken","year":"2002","journal-title":"FEBS Lett."},{"key":"2023013112130572000_B29","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1093\/bioinformatics\/btl060","article-title":"A systematic comparison and evaluation of biclustering methods for gene expression data","volume":"22","author":"Prelic","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112130572000_B30","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1105\/tpc.104.028282","article-title":"New subunits NDH-M, -N, and -O, encoded by nuclear genes, are essential for plastid Ndh complex functioning in higher plants","volume":"17","author":"Rumeau","year":"2005","journal-title":"Plant Cell"},{"key":"2023013112130572000_B31","doi-asserted-by":"crossref","first-page":"5659","DOI":"10.1091\/mbc.e04-04-0340","article-title":"Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress","volume":"15","author":"Shapira","year":"2004","journal-title":"Mol. Biol. Cell"},{"key":"2023013112130572000_B32","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nbt1239","article-title":"The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements","volume":"24","author":"Shi","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023013112130572000_B33","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1093\/pcp\/pcn058","article-title":"CRR23\/NdhL is a subunit of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis","volume":"49","author":"Shimizu","year":"2008","journal-title":"Plant Cell Physiol."},{"key":"2023013112130572000_B34","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1371\/journal.pcbi.0030042","article-title":"Deciphering protein-protein interactions. Part I. Experimental techniques and databases","volume":"3","author":"Shoemaker","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023013112130572000_B35","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Biol. Cell"},{"key":"2023013112130572000_B36","doi-asserted-by":"crossref","first-page":"3647","DOI":"10.1093\/bioinformatics\/bth398","article-title":"CSB.DB: a comprehensive systems-biology database","volume":"20","author":"Steinhauser","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112130572000_B37","doi-asserted-by":"crossref","first-page":"D1009","DOI":"10.1093\/nar\/gkm965","article-title":"The Arabidopsis Information Resource (TAIR): gene structure and function annotation","volume":"36","author":"Swarbreck","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112130572000_B38","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1111\/j.1365-313X.2005.02437.x","article-title":"The botany array resource: e-Northerns, expression angling, and promoter analyses","volume":"43","author":"Toufighi","year":"2005","journal-title":"Plant J."},{"key":"2023013112130572000_B39","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.tig.2006.01.006","article-title":"Similar gene expression profiles do not imply similar tissue functions","volume":"22","author":"Yanai","year":"2006","journal-title":"Trends Genet."},{"key":"2023013112130572000_B40","doi-asserted-by":"crossref","first-page":"26260","DOI":"10.1074\/jbc.M603582200","article-title":"The PsbQ protein is required in Arabidopsis for photosystem II assembly\/stability and photoautotrophy under low light conditions","volume":"281","author":"Yi","year":"2006","journal-title":"J. Biol. Chem."},{"key":"2023013112130572000_B41","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.tplants.2005.07.003","article-title":"Gene-expression analysis and network discovery using Genevestigator","volume":"10","author":"Zimmermann","year":"2005","journal-title":"Trends Plant Sci."},{"key":"2023013112130572000_B42","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1093\/clinchem\/39.4.561","article-title":"Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine","volume":"39","author":"Zweig","year":"1993","journal-title":"Clin. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/20\/2677\/48993865\/bioinformatics_25_20_2677.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/20\/2677\/48993865\/bioinformatics_25_20_2677.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:41:11Z","timestamp":1675201271000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/20\/2677\/192771"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,7,20]]},"references-count":42,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2009,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp442","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,10,15]]},"published":{"date-parts":[[2009,7,20]]}}}