Bioinformatics Advance Access originally published online on February 5, 2004
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.
Confirmation of data mining based predictions of protein function
Department of Computer Science, University of Wales, Aberystwyth, Wales, SY23 3DB, UK
Received on April 30, 2003; revised on July 25, 2003; accepted on August 28, 2003
Advance Access Publication February 5, 2004
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 Escherichia 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
Contact: rdk{at}aber.ac.uk
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Clare, A. Karwath, H. Ougham, and R. D. King Functional bioinformatics for Arabidopsis thaliana Bioinformatics, May 1, 2006; 22(9): 1130 - 1136. [Abstract] [Full Text] [PDF]
|
|