{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T21:49:12Z","timestamp":1791064152979,"version":"4.1.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Microarray experiments that allow simultaneous expression profiling of thousands of genes in various conditions (tissues, cells or time) generate data whose analysis raises difficult problems. In particular, there is a vast disproportion between the number of attributes (tens of thousands) and the number of examples (several tens). Dimension reduction is therefore a key step before applying classification approaches. Many methods have been proposed to this purpose, but only a few of them considered a direct quantification of transcriptional interactions. We describe and experimentally validate a new dimension reduction and feature construction method, which assesses interactions between expression profiles to improve microarray-based classification accuracy.<\/jats:p><jats:p>Results: Our approach relies on a mutual information measure that exposes some elementary constituents of the information contained in a pair of gene expression profiles. We show that their analysis implies a term that represents the information of the interaction between the two genes. The principle of our method, called FeatKNN, is to exploit the information provided by highly synergic gene pairs to improve classification accuracy. First, a heuristic search selects the most informative gene pairs. Then, for each selected pair, a new feature, representing the classification margin of a KNN classifier in the gene pairs space, is constructed. We show experimentally that the interactional information has a degree of significance comparable to that of the gene expression profiles considered separately. Our method has been tested with different classifiers and yielded significant improvements in accuracy on several public microarray databases. Moreover, a synthetic assessment of the biological significance of the concept of synergic gene pairs suggested its ability to uncover relevant mechanisms underlying interactions among various cellular processes.<\/jats:p><jats:p>Contact: \u00a0hanczar_blaise@yahoo.fr<\/jats:p><jats:p>Supplementary information: Complementary results can be found on the companion website at http:\/\/featknn.nutriomique.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm429","type":"journal-article","created":{"date-parts":[[2007,10,10]],"date-time":"2007-10-10T00:24:37Z","timestamp":1191975877000},"page":"2866-2872","source":"Crossref","is-referenced-by-count":18,"title":["Feature construction from synergic pairs to improve microarray-based classification"],"prefix":"10.1093","volume":"23","author":[{"given":"Blaise","family":"Hanczar","sequence":"first","affiliation":[{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Daniel","family":"Zucker","sequence":"additional","affiliation":[{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"},{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"},{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"},{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corneliu","family":"Henegar","sequence":"additional","affiliation":[{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"},{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"},{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorenza","family":"Saitta","sequence":"additional","affiliation":[{"name":"1 Laboratoire d'Informatique M\u00e9dicale et Bioinformatique (Lim & Bio), Universit\u00e9 Paris 13, 93017 Bobigny, 2Universit\u00e9 Paris Descarte, F-75006, 3Universit\u00e9 Pierre et Marie Curie - Paris 6, Centre de recherche des Cordeliers, UMR S 872, 4INSERM, U872, Paris, F-75006, France and 5Dipartimento di Informatica, Universit\u00e1 del Piemonte Orientale, 15100 Alessandria, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,10,9]]},"reference":[{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"6562","DOI":"10.1073\/pnas.102102699","article-title":"Selection bias in gene extraction on the basis of microarray gene expression data","volume":"99","author":"Ambroise","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107263960200_","volume-title":"Scoring genes for relevance","author":"Ben-Dor","year":"2000"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"research0017.1","DOI":"10.1186\/gb-2002-3-4-research0017","article-title":"New feature subset selection procedures for classification of expression profiles","volume":"3","author":"Bo","year":"2002","journal-title":"Genome Biology"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/bioinformatics\/btg419","article-title":"Is cross-validation valid for small-sample microarray classification?","volume":"20","author":"Braga-Neto","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041107263960200_","first-page":"418","article-title":"Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements","author":"Butte","year":"2000","journal-title":"Pac. Symp. Biocomput."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1147","article-title":"Dimension reduction for classification with gene expression microarray data","volume":"5","author":"Dai","year":"2006","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/S1368-7646(98)80046-0","article-title":"Cellular survival pathways and resistance to cancer therapy","volume":"1","author":"Dennis","year":"1998","journal-title":"Drug Resist. Updat."},{"key":"2023041107263960200_","first-page":"523","volume-title":"Proceedings of the IEEE Computer Society Conference on Bioinformatics","author":"Ding","year":"2003"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1198\/016214502753479248","article-title":"Comparison of discrimination methods for classification of tumors using gene expression data","volume":"97","author":"Dudoit","year":"2002","journal-title":"J. Am. Stat. Assoc."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1080\/01621459.1983.10477973","article-title":"Estimating the error rate of a prediction rule: improvement on cross-validation","volume":"78","author":"Efron","year":"1983","journal-title":"J. Am. Stat. Assoc."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1093\/bioinformatics\/16.10.906","article-title":"Support vector machine classification and validation of cancer tissue samples using microarray expression data","volume":"16","author":"Furey","year":"2000","journal-title":"Bioinformatics"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1071","article-title":"Classifying gene expression profiles from pairwise mRNA comparisons","volume":"3","author":"Geman","year":"2004","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1145\/980972.980977","article-title":"Improving classification of microarray data using prototype-based feature selection","volume":"5","author":"Hanczar","year":"2003","journal-title":"SIGKDD Explor."},{"key":"2023041107263960200_","first-page":"229","article-title":"Analyzing attribute dependencies","volume-title":"Proceedings A of the 7th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD)","author":"Jakulin","year":"2003"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"4803","DOI":"10.1242\/jcs.03270","article-title":"All in the CCN family: essential matricellular signaling modulators emerge from the bunker","volume":"119","author":"Leask","year":"2006","journal-title":"J. Cell. Sci"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/j.csda.2004.03.017","article-title":"An extensive comparison of recent classification tools applied to microarray data","volume":"48","author":"Lee","year":"2005","journal-title":"Comput. Stat. Data Analy"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"3096","DOI":"10.1103\/PhysRevE.62.3096","article-title":"Physical nature of higher-order mutual information: intrinsic correlations and frustration","volume":"62","author":"Matsuda","year":"2000","journal-title":"Phys. Rev. E"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-8-35","article-title":"Classification of microarray data using gene networks","volume":"8","author":"Rapaport","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023041107263960200_","first-page":"1371","article-title":"Overfitting in making comparisons between variable selection methods","volume":"3","author":"Reunanen","year":"2003","journal-title":"J. Mach. Learn. Res."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/416552a","article-title":"DNMT1 and DNMT3b cooperate to silence genes in human cancer cells","volume":"416","author":"Rhee","year":"2002","journal-title":"Nature"},{"key":"2023041107263960200_","first-page":"322","article-title":"Boosting the margin: a new explanation for the effectiveness of voting methods","volume-title":"Proceedings 14th International Conference on Machine Learning","author":"Schapire","year":"1997"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1002\/j.1538-7305.1948.tb00917.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Sys. Tech. J."},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1093\/bioinformatics\/18.suppl_2.S231","article-title":"The mutual information: detecting and evaluating dependencies between variables","volume":"18","author":"Steuer","year":"2002","journal-title":"Bioinformatics"},{"key":"2023041107263960200_","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.compbiolchem.2004.11.001","article-title":"Gene selection from microarray data for cancer classification \u2013 a machine learning approach","volume":"29","author":"Wang","year":"2005","journal-title":"Comput. Biol. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/21\/2866\/49821069\/bioinformatics_23_21_2866.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/21\/2866\/49821069\/bioinformatics_23_21_2866.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T11:01:47Z","timestamp":1684062107000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/21\/2866\/372089"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,10,9]]},"references-count":24,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2007,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm429","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,11,1]]},"published":{"date-parts":[[2007,10,9]]}}}