{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T17:40:21Z","timestamp":1686764421444},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1693,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: A reconstruction of full-length transcripts observed by next-generation sequencer or tiling arrays is an essential technique to know all phenomena of transcriptomes. Several techniques of the reconstruction have been developed. However, problems of high-level noises and biases still remain and interrupt the reconstruction. A method is required that is robust against noise and bias and correctly reconstructs transcripts regardless of equipment used.<\/jats:p><jats:p>Results: We propose a completely new statistical method that reconstructs full-length transcripts and can be applied on both next-generation sequencers and tiling arrays. The method called ARTADE2 analyzes \u2018positional correlation\u2019, meaning correlations of expression values for every combination on genomic positions of multiple transcriptional data. ARTADE2 then reconstructs full-length transcripts using a logistic model based on the positional correlation and the Markov model. ARTADE2 elucidated 17 591 full-length transcripts from 55 transcriptome datasets and showed notable performance compared with other recent prediction methods. Moreover, 1489 novel transcripts were discovered. We experimentally tested 16 novel transcripts, among which 14 were confirmed by reverse transcription\u2013polymerase chain reaction and sequence mapping. The method also showed notable performance for reconstructing of mRNA observed by a next-generation sequencer. Moreover, the positional correlation and factor analysis embedded in ARTADE2 successfully detected regions at which alternative isoforms may exist, and thus are expected to be applied for discovering transcript biomarkers for a wide range of disciplines including preemptive medicine.<\/jats:p><jats:p>Availability: \u00a0http:\/\/matome.base.riken.jp<\/jats:p><jats:p>Contact: \u00a0toyoda@base.riken.jp<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts065","type":"journal-article","created":{"date-parts":[[2012,2,14]],"date-time":"2012-02-14T01:23:09Z","timestamp":1329182589000},"page":"929-937","source":"Crossref","is-referenced-by-count":5,"title":["Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads"],"prefix":"10.1093","volume":"28","author":[{"given":"Shuji","family":"Kawaguchi","sequence":"first","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kei","family":"Iida","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erimi","family":"Harada","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kousuke","family":"Hanada","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"},{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akihiro","family":"Matsui","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masanori","family":"Okamoto","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuo","family":"Shinozaki","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Motoaki","family":"Seki","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tetsuro","family":"Toyoda","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Systems Engineering division, RIKEN Yokohama Institute and 2RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,2,13]]},"reference":[{"key":"2023012512210488900_B1","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1126\/science.1157956","article-title":"Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics","volume":"320","author":"Baerenfaller","year":"2008","journal-title":"Science"},{"key":"2023012512210488900_B2","doi-asserted-by":"crossref","first-page":"21034","DOI":"10.1073\/pnas.0811066106","article-title":"Discovery and revision of Arabidopsis genes by proteogenomics","volume":"105","author":"Castellana","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512210488900_B3","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/nprot.2009.8","article-title":"Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome","volume":"4","author":"German","year":"2009","journal-title":"Nat. Protoc."},{"key":"2023012512210488900_B4","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1101\/gr.089060.108","article-title":"Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function","volume":"19","author":"Grobei","year":"2009","journal-title":"Genome Res."},{"key":"2023012512210488900_B5","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1111\/j.2044-8317.1964.tb00244.x","article-title":"PROMAX : a quick method for rotation to oblique simple structure","volume":"17","author":"Hendrickson","year":"1964","journal-title":"Br. J. Stat. Psychol."},{"key":"2023012512210488900_B6","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/pcp\/pcq202","article-title":"ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic-structure-based dynamic expression (DSDE) analyses","volume":"52","author":"Iida","year":"2011","journal-title":"Plant Cell Physiol."},{"key":"2023012512210488900_B7","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/BF02289233","article-title":"The varimax criterion for analytic rotation in factor analysis","volume":"23","author":"Kaiser","year":"1958","journal-title":"Psychometrika"},{"key":"2023012512210488900_B8","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1093\/bioinformatics\/btn054","article-title":"Statistical search on the Semantic Web","volume":"24","author":"Kobayashi","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512210488900_B9","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/nmeth0306-211","article-title":"CAGE: cap analysis of gene expression","volume":"3","author":"Kodzius","year":"2006","journal-title":"Nat. Methods"},{"key":"2023012512210488900_B10","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.cell.2008.03.029","article-title":"Highly integrated single-base resolution maps of the epigenome in Arabidopsis","volume":"133","author":"Lister","year":"2008","journal-title":"Cell"},{"key":"2023012512210488900_B11","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1093\/pcp\/pcn101","article-title":"Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array","volume":"49","author":"Matsui","year":"2008","journal-title":"Plant Cell Physiol."},{"key":"2023012512210488900_B12","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1186\/1471-2164-11-681","article-title":"De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq","volume":"11","author":"Mizrachi","year":"2010","journal-title":"BMC Genomics"},{"key":"2023012512210488900_B13","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2023012512210488900_B14","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/j.1365-313X.2010.04135.x","article-title":"Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays","volume":"62","author":"Okamoto","year":"2010","journal-title":"Plant J."},{"key":"2023012512210488900_B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/msb.2009.68","article-title":"Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis","volume":"5","author":"Piques","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"2023012512210488900_B16","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1104\/pp.109.138677","article-title":"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks","volume":"150","author":"Reiland","year":"2009","journal-title":"Plant Physiol."},{"key":"2023012512210488900_B17","doi-asserted-by":"crossref","first-page":"R22","DOI":"10.1186\/gb-2011-12-3-r22","article-title":"Improving RNA-Seq expression estimates by correcting for fragment bias","volume":"12","author":"Roberts","year":"2011","journal-title":"Genome Biol."},{"key":"2023012512210488900_B18","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1093\/bioinformatics\/btr355","article-title":"Identification of novel transcripts in annotated genomes using RNA-Seq","volume":"27","author":"Roberts","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512210488900_B19","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.tig.2005.06.007","article-title":"Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping","volume":"8","author":"Royce","year":"2005","journal-title":"Trends Genet."},{"key":"2023012512210488900_B20","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1093\/bioinformatics\/btm052","article-title":"Assessing the need for sequence-based normalization in tiling microarray experiments","volume":"23","author":"Royce","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512210488900_B21","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1038\/35057141","article-title":"Experimental annotation of the human genome using microarray technology","volume":"409","author":"Shoemaker","year":"2001","journal-title":"Nature"},{"issue":"Suppl. 2","key":"2023012512210488900_B22","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1093\/bioinformatics\/btg1080","article-title":"Gene prediction with a hidden Markov model and a new intron submodel","volume":"19","author":"Stanke","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012512210488900_B23","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1093\/bioinformatics\/bth165","article-title":"Omic space: coordinate-based integration and analysis of genomic phenomic interactions","volume":"20","author":"Toyoda","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012512210488900_B24","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1111\/j.1365-313X.2005.02470.x","article-title":"Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models","volume":"43","author":"Toyoda","year":"2005","journal-title":"Plant J."},{"key":"2023012512210488900_B25","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512210488900_B26","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023012512210488900_B27","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1007\/978-1-4615-4397-8_3","article-title":"Construct explication through factor or component analysis: A review and evaluation of alternative procedures for determining the number of factors or components","volume-title":"Problems and solutions in human assessment: Honoring Douglas N. Jackson at seventy","author":"Velicer","year":"2000"},{"key":"2023012512210488900_B28","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/nature10158","article-title":"Genome sequence and analysis of the tuber crop potato","volume":"475","author":"Xu","year":"2011","journal-title":"Nature"},{"key":"2023012512210488900_B29","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1126\/science.1088305","article-title":"Empirical analysis of transcriptional activity in the Arabidopsis genome","volume":"302","author":"Yamada","year":"2003","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/929\/48874417\/bioinformatics_28_7_929.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/929\/48874417\/bioinformatics_28_7_929.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T17:19:53Z","timestamp":1686763193000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/7\/929\/209757"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2,13]]},"references-count":29,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2012,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts065","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,4,1]]},"published":{"date-parts":[[2012,2,13]]}}}