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Classification of nuclear receptors based on amino acid composition and dipeptide composition.

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title Classification of nuclear receptors based on amino acid composition and dipeptide composition.
 
Creator Bhasin, Manoj
Raghava, G.P.S.
 
Subject QD Chemistry
 
Description Nuclear receptors are key transcription factors that regulate crucial gene networks responsible for cell growth, differentiation, and homeostasis. Nuclear receptors form a superfamily of phylogenetically related proteins and control functions associated with major diseases (e.g. diabetes, osteoporosis, and cancer). In this study, a novel method has been developed for classifying the subfamilies of nuclear receptors. The classification was achieved on the basis of amino acid and dipeptide composition from a sequence of receptors using support vector machines. The training and testing was done on a non-redundant data set of 282 proteins obtained from the NucleaRDB data base (1). The performance of all classifiers was evaluated using a 5-fold cross validation test. In the 5-fold cross-validation, the data set was randomly partitioned into five equal sets and evaluated five times on each distinct set while keeping the remaining four sets for training. It was found that different subfamilies of nuclear receptors were quite closely correlated in terms of amino acid composition as well as dipeptide composition. The overall accuracy of amino acid composition-based and dipeptide composition-based classifiers were 82.6 and 97.5%, respectively. Therefore, our results prove that different subfamilies of nuclear receptors are predictable with considerable accuracy using amino acid or dipeptide composition. Furthermore, based on above approach, an online web service, NRpred, was developed, which is available at www.imtech.res.in/raghava/nrpred.
 
Publisher ASBMB
 
Date 2004-05-28
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/218/1/raghava2004.3.pdf
Bhasin, Manoj and Raghava, G.P.S. (2004) Classification of nuclear receptors based on amino acid composition and dipeptide composition. The Journal of biological chemistry, 279 (22). pp. 23262-6. ISSN 0021-9258
 
Relation http://www.jbc.org/content/279/22/23262.full.pdf+html
http://crdd.osdd.net/open/218/