{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T04:29:14Z","timestamp":1778646554293,"version":"3.51.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2984,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Functional characterization of genes is of great importance for the understanding of complex cellular processes. Valuable information for this purpose can be obtained from pathway databases, like KEGG. However, only a small fraction of genes is annotated with pathway information up to now. In contrast, information on contained protein domains can be obtained for a significantly higher number of genes, e.g. from the InterPro database.<\/jats:p><jats:p>Results: We present a classification model, which for a specific gene of interest can predict the mapping to a KEGG pathway, based on its domain signature. The classifier makes explicit use of the hierarchical organization of pathways in the KEGG database. Furthermore, we take into account that a specific gene can be mapped to different pathways at the same time. The classification method produces a scoring of all possible mapping positions of the gene in the KEGG hierarchy. Evaluations of our model, which is a combination of a SVM and ranking perceptron approach, show a high prediction performance. Moreover, for signaling pathways we reveal that it is even possible to forecast accurately the membership to individual pathway components.<\/jats:p><jats:p>Availability: The R package gene2pathway is a supplement to this article.<\/jats:p><jats:p>Contact: \u00a0h.froehlich@dkfz-heidelberg.de<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn403","type":"journal-article","created":{"date-parts":[[2008,8,3]],"date-time":"2008-08-03T00:13:13Z","timestamp":1217722393000},"page":"2137-2142","source":"Crossref","is-referenced-by-count":16,"title":["Predicting pathway membership via domain signatures"],"prefix":"10.1093","volume":"24","author":[{"given":"Holger","family":"Fr\u00f6hlich","sequence":"first","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Fellmann","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Holger","family":"S\u00fcltmann","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Annemarie","family":"Poustka","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Bei\u00dfbarth","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,8,1]]},"reference":[{"key":"2023020211122671300_B1","doi-asserted-by":"crossref","first-page":"1610","DOI":"10.1016\/j.jacc.2006.07.026","article-title":"Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies","author":"Barth","year":"2006","journal-title":"J. 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