Confirmation of Data Mining Based Predictions of Protein Function

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dc.contributor.author King, Ross Donald
dc.contributor.author Wise, P. H.
dc.contributor.author Clare, Amanda
dc.date.accessioned 2006-04-24T15:20:05Z
dc.date.available 2006-04-24T15:20:05Z
dc.date.issued 2004
dc.identifier.citation King , R D , Wise , P H & Clare , A 2004 , ' Confirmation of Data Mining Based Predictions of Protein Function ' Bioinformatics , vol 20 , no. 7 , pp. 1110-1118 . en
dc.identifier.other PURE: 68050
dc.identifier.other dspace: 2160/128
dc.identifier.uri http://hdl.handle.net/2160/128
dc.description King, R. D. and Wise, P. H. and Clare, A. (2004) Confirmation of Data Mining Based Predictions of Protein Function. Bioinformatics 20(7), 1110-1118 en
dc.description.abstract Motivation: A central problem in bioinformatics is the assignment of function to sequenced open reading frames (ORFs). The most common approach is based on inferred homology using a statistically based sequence similarity (SIM) method e.g. PSI-BLAST. Alternative non-SIM based bioinformatic methods are becoming popular. One such method is Data Mining Prediction (DMP). This is based on combining evidence from amino-acid attributes, predicted structure, and phylogenic patterns; and uses a combination of Inductive Logic Programming data mining, and decision trees to produce prediction rules for functional class. DMP predictions are more general than is possible using homology. In 2000/1 DMP was used to make public predictions of the function of 1309 E. coli ORFs. Since then biological knowledge has advanced allowing us to test our predictions. Results: We examined the updated (20.02.02) Riley group genome annotation, and examined the scientific literature for direct experimental derivations of ORF function. Both tests confirmed the DMP predictions. Accuracy varied between rules, and with the detail of prediction, but they were generally significantly better than random. For voting rules, accuracies of 75-100% were obtained. Twenty one of these DMP predictions have been confirmed by direct experimentation. The DMP rules also have interesting biological explanations. DMP is, to the best of our knowledge, the first non-SIM based prediction method to have been tested directly on new data. Availability: We have designed the ``Genepredictions'' database for protein functional predictions. This is intended to act as an open repository for predictions for any organism and can be accessed at http://www.genepredictions.org. en
dc.format.extent 9 en
dc.language.iso eng
dc.relation.ispartof Bioinformatics en
dc.title Confirmation of Data Mining Based Predictions of Protein Function en
dc.type Text en
dc.type.publicationtype Article (Journal) en
dc.contributor.institution Department of Computer Science en
dc.contributor.institution Bioinformatics and Computational Biology Group en
dc.description.status Peer reviewed en


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