{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:19:44Z","timestamp":1674710384355},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2488,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Inferring genetic or transcriptional interactions, when done successfully, may provide insights into biological processes or biochemical pathways of interest. Unfortunately, most computational algorithms require a certain level of programming expertise. To provide a simple web interface for users to infer interactions from time course gene expression data, we present WebPARE, which is based on the pattern recognition algorithm (PARE). For expression data, in which each type of interaction (e.g. activator target) and the corresponding paired gene expression pattern are significantly associated, PARE uses a non-linear score to classify gene pairs of interest into a few subclasses of various time lags. In each subclass, PARE learns the parameters in the decision score using known interactions from biological experiments or published literature. Subsequently, the trained algorithm predicts interactions of a similar nature. Previously, PARE was shown to infer two sets of interactions in yeast successfully. Moreover, several predicted genetic interactions coincided with existing pathways; this indicates the potential of PARE in predicting partial pathway components. Given a list of gene pairs or genes of interest and expression data, WebPARE invokes PARE and outputs predicted interactions and their networks in directed graphs.<\/jats:p>\n               <jats:p>Availability: A web-computing service WebPARE is publicly available at: http:\/\/www.stat.sinica.edu.tw\/WebPARE<\/jats:p>\n               <jats:p>Contact: \u00a0gshieh@stat.sinica.edu.tw<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp684","type":"journal-article","created":{"date-parts":[[2009,12,11]],"date-time":"2009-12-11T01:51:16Z","timestamp":1260496276000},"page":"582-584","source":"Crossref","is-referenced-by-count":1,"title":["WebPARE: web-computing for inferring genetic or transcriptional interactions"],"prefix":"10.1093","volume":"26","author":[{"given":"Cheng-Long","family":"Chuang","sequence":"first","affiliation":[{"name":"1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan and 2 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan"},{"name":"1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan and 2 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan"}]},{"given":"Jia-Hong","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan and 2 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan"}]},{"given":"Chi-Sheng","family":"Cheng","sequence":"additional","affiliation":[{"name":"1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan and 2 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan"}]},{"given":"Grace S.","family":"Shieh","sequence":"additional","affiliation":[{"name":"1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan and 2 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan"},{"name":"1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan and 2 Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2009,12,10]]},"reference":[{"key":"2023012508030015800_B1","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/nrg2085","article-title":"Exploring genetic interactions and networks with yeast","volume":"8","author":"Boone","year":"2007","journal-title":"Nat. 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Genet."},{"key":"2023012508030015800_B2","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1093\/bioinformatics\/btn098","article-title":"A pattern recognition approach to infer time-lagged genetic interactions","volume":"24","author":"Chuang","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508030015800_B3","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/nature07423","article-title":"Somatic mutations affect key pathways in lung adenocarcinoma","volume":"455","author":"Ding","year":"2008","journal-title":"Nature"},{"key":"2023012508030015800_B4","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1038\/nature06955","article-title":"Global control of cell-cycle transcription by coupled CDK and network oscillators","volume":"453","author":"Orlando","year":"2008","journal-title":"Nature"},{"key":"2023012508030015800_B5","doi-asserted-by":"crossref","first-page":"3056","DOI":"10.1093\/bioinformatics\/btm465","article-title":"Inferring transcriptional regulatory networks from high-throughput data","volume":"23","author":"Wang","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012508030015800_B6","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/4\/582\/48855500\/bioinformatics_26_4_582.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/4\/582\/48855500\/bioinformatics_26_4_582.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:04:02Z","timestamp":1674633842000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/4\/582\/243223"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12,10]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2010,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp684","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,2,15]]},"published":{"date-parts":[[2009,12,10]]}}}