{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T05:55:47Z","timestamp":1760853347275},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3126,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: For any time-course microarray data in which the gene interactions and the associated paired patterns are dependent, the proposed pattern recognition (PARE) approach can infer time-lagged genetic interactions, a challenging task due to the small number of time points and large number of genes. PARE utilizes a non-linear score to identify subclasses of gene pairs with different time lags. In each subclass, PARE extracts non-linear characteristics of paired gene-expression curves and learns weights of the decision score applying an optimization algorithm to microarray gene-expression data (MGED) of some known interactions, from biological experiments or published literature. Namely, PARE integrates both MGED and existing knowledge via machine learning, and subsequently predicts the other genetic interactions in the subclass.<\/jats:p>\n               <jats:p>Results: PARE, a time-lagged correlation approach and the latest advance in graphical Gaussian models were applied to predict 112 (132) pairs of TC\/TD (transcriptional regulatory) interactions. Checked against qRT-PCR results (published literature), their true positive rates are 73% (77%), 46% (51%), and 52% (59%), respectively. The false positive rates of predicting TC and TD (AT and RT) interactions in the yeast genome are bounded by 13 and 10% (10 and 14%), respectively. Several predicted TC\/TD interactions are shown to coincide with existing pathways involving Sgs1, Srs2 and Mus81. This reinforces the possibility of applying genetic interactions to predict pathways of protein complexes. Moreover, some experimentally testable gene interactions involving DNA repair are predicted.<\/jats:p>\n               <jats:p>Availability: Supplementary data and PARE software are available at http:\/\/www.stat.sinica.edu.tw\/~gshieh\/pare.htm.<\/jats:p>\n               <jats:p>Contact: \u00a0gshieh@stat.sinica.edu.tw<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn098","type":"journal-article","created":{"date-parts":[[2008,3,13]],"date-time":"2008-03-13T00:13:54Z","timestamp":1205367234000},"page":"1183-1190","source":"Crossref","is-referenced-by-count":29,"title":["A pattern recognition approach to infer time-lagged genetic interactions"],"prefix":"10.1093","volume":"24","author":[{"given":"Cheng-Long","family":"Chuang","sequence":"first","affiliation":[{"name":"1 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, 2Institute of Statistical Science, Academia Sinica, Taipei 115 and 3Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan"},{"name":"1 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, 2Institute of Statistical Science, Academia Sinica, Taipei 115 and 3Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chih-Hung","family":"Jen","sequence":"additional","affiliation":[{"name":"1 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, 2Institute of Statistical Science, Academia Sinica, Taipei 115 and 3Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chung-Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, 2Institute of Statistical Science, Academia Sinica, Taipei 115 and 3Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grace S.","family":"Shieh","sequence":"additional","affiliation":[{"name":"1 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, 2Institute of Statistical Science, Academia Sinica, Taipei 115 and 3Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan"},{"name":"1 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, 2Institute of Statistical Science, Academia Sinica, Taipei 115 and 3Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,3,12]]},"reference":[{"key":"2023020210051254200_B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/S1532-0464(03)00031-5","article-title":"Revising regulatory networks: from expression data to linear causal models","volume":"35","author":"Bay","year":"2002","journal-title":"J. Biomed. Inform"},{"key":"2023020210051254200_B2","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0076-6879(06)08006-2","article-title":"Use of yeast for detection of endogenous abasic lesions, their source, and their repair","volume":"408","author":"Boiteux","year":"2006","journal-title":"Methods Enzymol"},{"key":"2023020210051254200_B3","article-title":"A pattern recognition approach to infer genetic networks","volume-title":"Technical Report C2005-05.","author":"Chuang","year":"2005"},{"key":"2023020210051254200_B4","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/nature05649","article-title":"Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map","volume":"446","author":"Collins","year":"2007","journal-title":"Nature"},{"key":"2023020210051254200_B5","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.jmva.2004.02.009","article-title":"Sparse graphical models for exploring gene expression data","volume":"90","author":"Dobra","year":"2004","journal-title":"J. Multiv. Anal"},{"key":"2023020210051254200_B6","first-page":"4522","article-title":"CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context","volume":"14","author":"Draper","year":"1994","journal-title":"Mol. Cell. Biol"},{"key":"2023020210051254200_B7","first-page":"39","article-title":"A new optimizer using particle swarm theory","author":"Eberhart","year":"1995"},{"key":"2023020210051254200_B8","doi-asserted-by":"crossref","first-page":"16887","DOI":"10.1073\/pnas.252652399","article-title":"Alternate pathways involving Sgs1\/Top3, Mus81\/Mms4, and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication","volume":"99","author":"Fabre","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210051254200_B9","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.1101\/gad.1105203","article-title":"Slx1-Slx4 is a second structure-specific endonu-clease functionally redundant with Sgs1-Top3","volume":"17","author":"Fricke","year":"2003","journal-title":"Genes Dev"},{"key":"2023020210051254200_B10","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1094068","article-title":"Inferring cellular networks using probabilistic graphical models","volume":"303","author":"Friedman","year":"2004","journal-title":"Science"},{"key":"2023020210051254200_B11","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1128\/MMBR.62.2.334-361.1998","article-title":"Yeast carbon catabolite repression","volume":"62","author":"Gancedo","year":"1998","journal-title":"Microbiol. Mol. Biol. Rev"},{"key":"2023020210051254200_B12","volume-title":"Digital Image Processing.","author":"Gonzalez","year":"2002"},{"key":"2023020210051254200_B13","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1126\/science.1056072","article-title":"Principles for the buffering of genetic variation","volume":"291","author":"Hartman","year":"2001","journal-title":"Science"},{"key":"2023020210051254200_B14","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1038\/ng0704-664","article-title":"A gene network for navigating the literature","volume":"36","author":"Hoffmann","year":"2004","journal-title":"Nat. Genet"},{"key":"2023020210051254200_B15","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1093\/bioinformatics\/btg313","article-title":"Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks","volume":"19","author":"Husmeier","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020210051254200_B16","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/ng1523","article-title":"Transcription control reprogramming in genetic backup circuits","volume":"37","author":"Kafri","year":"2005","journal-title":"Nat. Genet"},{"key":"2023020210051254200_B17","first-page":"83","article-title":"Correspondence analysis of genes and tissue types and finding genetic links from microarray data","volume":"11","author":"Kishino","year":"2000","journal-title":"Genome Inform"},{"key":"2023020210051254200_B18","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1534\/genetics.106.067801","article-title":"Brc1-mediated rescue of Smc5\/6 deficiency: requirement for multiple nucleases and a novel Rad18 function","volume":"175","author":"Lee","year":"2007","journal-title":"Genetics"},{"key":"2023020210051254200_B19","doi-asserted-by":"crossref","first-page":"R37","DOI":"10.1186\/gb-2006-7-5-r37","article-title":"Inferring transcriptional modules from ChIP-chip, motif and mircoarray data","volume":"7","author":"Lemmens","year":"2006","journal-title":"Genome Biol"},{"key":"2023020210051254200_B20","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1534\/genetics.167.1.35","article-title":"Analysis of beta-1,3-glucan assembly in Saccharomyces cerevisiae using a synthetic interaction network and altered sensitivity to caspofungin","volume":"167","author":"Lesage","year":"2004","journal-title":"Genetics"},{"key":"2023020210051254200_B21","doi-asserted-by":"crossref","first-page":"4086","DOI":"10.1128\/MCB.00136-06","article-title":"Sgs1 regulates gene conversion tract lengths and cross-overs independently of its helicase activity","volume":"26","author":"Lo","year":"2006","journal-title":"Mol. Cell. Biol"},{"key":"2023020210051254200_B22","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1093\/genetics\/157.4.1531","article-title":"The short life span of Saccharomyces cerevisiae sgs1 and srs2 mutants is a composite of normal aging processes and mitotic arrest due to defective recombination","volume":"157","author":"McVey","year":"2001","journal-title":"Genetics"},{"key":"2023020210051254200_B23","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1093\/nar\/27.1.44","article-title":"MIPS: a database for genomes and protein sequences","volume":"27","author":"Mewes","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023020210051254200_B24","volume-title":"Statistical Digital Signal Processing and Modeling.","author":"Monson","year":"1996"},{"key":"2023020210051254200_B25","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1007\/s004380000358","article-title":"Involvement of SGS1 in DNA damage-induced heteroallelic recombination that requires RAD52 in Saccharomyces cerevisiae","volume":"264","author":"Onoda","year":"2001","journal-title":"Mol. Gen. Genet"},{"key":"2023020210051254200_B26","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1038\/ng1258","article-title":"DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray","volume":"35","author":"Ooi","year":"2003","journal-title":"Nat. Genet"},{"key":"2023020210051254200_B27","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1016\/j.cell.2005.12.036","article-title":"A DNA integrity network in the yeast Saccharomyces cerevisiae","volume":"124","author":"Pan","year":"2006","journal-title":"Cell"},{"key":"2023020210051254200_B28","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1006\/jmbi.2000.5219","article-title":"Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles indentified new, biologically relevant interactions","volume":"314","author":"Qian","year":"2001","journal-title":"J. Mol. Biol"},{"key":"2023020210051254200_B29","first-page":"5","article-title":"Approaching causality: discovering time-lag correlations in genetic expression data with static and dynamic relevance networks","volume-title":"Proceedings of RECOMB 2000.","author":"Reis","year":"2000"},{"key":"2023020210051254200_B30","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/bti062","article-title":"An empirical Bayes approach to inferring large-scale gene association networks","volume":"21","author":"Sch\u00e4fer","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020210051254200_B31","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1128\/MCB.24.8.3213-3226.2004","article-title":"Requirement of Rrm3 helicase for repair of spontaneous DNA lesions in cells lacking Srs2 or Sgs1 helicase","volume":"24","author":"Schmidt","year":"2004","journal-title":"Mol. Cell. Biol"},{"key":"2023020210051254200_B32","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1101\/gr.2439804","article-title":"Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data","volume":"14","author":"Schmitt","year":"2004","journal-title":"Genome Res"},{"key":"2023020210051254200_B33","first-page":"357","article-title":"A regression approach to reconstruct gene networks","volume-title":"Proceedings of 2004 Taipei Sympisium on Statistical Genome.","author":"Shieh","year":"2004"},{"key":"2023020210051254200_B34","article-title":"A stepwise structural equation modeling algorithm to reconstruct genetic networks","volume-title":"Technical Report C2005-04.","author":"Shieh","year":"2005"},{"key":"2023020210051254200_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 Sarcharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Biol. Cell"},{"key":"2023020210051254200_B36","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1093\/bioinformatics\/18.2.287","article-title":"Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling","volume":"18","author":"Toh","year":"2002","journal-title":"Bioinformatics"},{"key":"2023020210051254200_B37","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1023\/A:1020337311471","article-title":"System for automatically inferring a genetic network from expression profiles","volume":"28","author":"Toh","year":"2002","journal-title":"J. Biol. Phys"},{"key":"2023020210051254200_B38","doi-asserted-by":"crossref","first-page":"2364","DOI":"10.1126\/science.1065810","article-title":"Systematic genetic analysis with ordered arrays of Yeast deletion mutants","volume":"294","author":"Tong","year":"2001","journal-title":"Science"},{"key":"2023020210051254200_B39","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1126\/science.1091317","article-title":"Global mapping of the Yeast genetic interaction network","volume":"303","author":"Tong","year":"2004","journal-title":"Science"},{"key":"2023020210051254200_B40","doi-asserted-by":"crossref","first-page":"13532","DOI":"10.1073\/pnas.0505874102","article-title":"Statistical methods for identifying yeast cell cycle transcription factors","volume":"12","author":"Tsai","year":"2005","journal-title":"Proc. Natl Acad. Sci"},{"key":"2023020210051254200_B41","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1093\/bioinformatics\/btl160","article-title":"Method for identifying transcription factor binding sites in yeast","volume":"22","author":"Tsai","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020210051254200_B42","first-page":"129","article-title":"Cluster inferences methods and graphical models evaluated on NCI60 microarray gene expression data","volume":"11","author":"Waddell","year":"2000","journal-title":"Genome Inform"},{"key":"2023020210051254200_B43","volume-title":"Graphical Models in Applied Multivariate Statistics.","author":"Whittaker","year":"1990"},{"key":"2023020210051254200_B44","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1093\/biomet\/90.4.809","article-title":"Efficient estimation of covariance selection models","volume":"90","author":"Wang","year":"2003","journal-title":"Biometrika"},{"key":"2023020210051254200_B45","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1534\/genetics.105.046060","article-title":"Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in saccharomyces cerevisiae","volume":"171","author":"Wong","year":"2005","journal-title":"Genetics"},{"key":"2023020210051254200_B46","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/j.tig.2005.06.006","article-title":"Discovering functional relationships: biochemistry versus genetics","volume":"21","author":"Wong","year":"2005","journal-title":"Trends Genet"},{"key":"2023020210051254200_B47","first-page":"63","article-title":"Interactive analysis of gene interactions using graphical Gaussian model","volume-title":"Proceedings of the ACM SIGKDD Workshop on Data Mining in Bioinformatics.","author":"Wu","year":"2003"},{"key":"2023020210051254200_B48","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1128","article-title":"A general framework for weighted gene co-expression networks analysis","volume":"4","author":"Zhang","year":"2005","journal-title":"Stat. Appl. Genet. Mol. Biol"},{"key":"2023020210051254200_B49","doi-asserted-by":"crossref","first-page":"7082","DOI":"10.1128\/MCB.24.16.7082-7090.2004","article-title":"Mrc1 is required for sister chromatid cohesion to aid in recombination repair of spontaneous damage","volume":"24","author":"Xu","year":"2004","journal-title":"Mol. Cell. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/9\/1183\/49047181\/bioinformatics_24_9_1183.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/9\/1183\/49047181\/bioinformatics_24_9_1183.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:37:14Z","timestamp":1675337834000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/9\/1183\/207406"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,3,12]]},"references-count":49,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2008,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn098","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,5,1]]},"published":{"date-parts":[[2008,3,12]]}}}