CART classification of human 5 ' UTR sequences

Davuluri, R. V., Suzuki, Y., Sugano, S., Zhang, M. Q. (November 2000) CART classification of human 5 ' UTR sequences. Genome Research, 10 (11). pp. 1807-1816. ISSN 1088-9051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/11076865
DOI: 10.1101/gr.GR-1460R

Abstract

A nonredundant database of 2312 full-length human 5'-untranslated regions (UTRs) was carefully prepared using state-of-the-art experimental and computational technologies. A comprehensive computational analysis of this data was conducted for characterizing the 5' UTR Features. Classification and regression tree (CART) analysis was used to classify the data into three distinct classes. Class I consists of mRNAs that are believed to be poorly translated with long 5' UTRs filled with potential inhibitory features. Class II consists of terminal oligopyrimidine tract (TOP) mRNAs that are regulated in a growth-dependent manner, and class III consists of mRNAs with Favorable 5' UTR features that may help efficient translation. The most accurate tree we found has 92.5% classification accuracy as estimated by cross validation. The classification model included the presence of TOP, a secondary structure, 5' UTR length, and the presence of upstream AUGs (uAUGs) as the most relevant variables. The present classification and characterization of the 5' UTRs provide precious information for better understanding the translational regulation of human mRNAs. Furthermore, this database and classification can help people build better computational models for predicting the 5'-terminal exon and separating the 5' UTR from the coding region.

Item Type: Paper
Uncontrolled Keywords: EUKARYOTIC MESSENGER-RNAS TRANSLATIONAL CONTROL SECONDARY STRUCTURE PROTEIN-SYNTHESIS CODON USAGE INITIATION EFFICIENCY EXPRESSION POSITION-+5 PREDICTION
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mRNA dynamics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mRNA
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: November 2000
Date Deposited: 31 Jan 2014 16:30
Last Modified: 31 Jan 2014 16:30
PMCID: PMC310970
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29361

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