5201585a - European Journal of Human Genetics (2006) 14,...

Info iconThis preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
ARTICLE A text-mining analysis of the human phenome Marc A van Driel 1 , Jorn Bruggeman 2 , Gert Vriend 1 , Han G Brunner* ,3 and Jack AM Leunissen 2 1 Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, the Netherlands; 2 Department of Bioinformatics, Wageningen University and Research Centre, Dreijenlaan 3, 6703HA Wageningen, the Netherlands; 3 Department of Human Genetics, University Medical Centre Nijmegen, Geert Grooteplein 10, 6525GA Nijmegen, the Netherlands A number of large-scale efforts are underway to define the relationships between genes and proteins in various species. But, few attempts have been made to systematically classify all such relationships at the phenotype level. Also, it is unknown whether such a phenotype map would carry biologically meaningful information. We have used text mining to classify over 5000 human phenotypes contained in the Online Mendelian Inheritance in Man database. We find that similarity between phenotypes reflects biological modules of interacting functionally related genes. These similarities are positively correlated with a number of measures of gene function, including relatedness at the level of protein sequence, protein motifs, functional annotation, and direct protein–protein interaction. Phenotype grouping reflects the modular nature of human disease genetics. Thus, phenotype mapping may be used to predict candidate genes for diseases as well as functional relations between genes and proteins. Such predictions will further improve if a unified system of phenotype descriptors is developed. The phenotype similarity data are accessible through a web interface at http://www.cmbi.ru.nl/MimMiner/. European Journal of Human Genetics (2006) 14, 535–542. doi:10.1038/sj.ejhg.5201585; published online 22 February 2006 Keywords: phenome; text mining; candidate disease genes; phenotype–genotype relations Introduction Functional annotation of genes is an important challenge once the sequence of a genome has been completed. Gene annotation encompasses a variety of functional attributes, from structural motifs, through cellular function, to associations with specific functions and processes at the level of the organism. Apart from descriptors at the gene and protein level, the phenotype effect of a mutated or deleted gene forms part of its functional annotation. Systematic mutation and RNA interference screens have been performed for selected phenotypes in Drosophila. melanogaster , Caenorhabditis. elegans , and Saccharomyces. cerevisiae . 1–3 Also for Mus. musculus , an ambitious project to mutagenize most or all genes has been conceived. 4 Previous studies have correlated various attributes of human genes, such as predicted function or amino-acid sequence length, with the chance of causing a disease. 5–7
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 06/14/2011 for the course DATABASE - taught by Professor - during the Spring '11 term at Aarhus Universitet.

Page1 / 8

5201585a - European Journal of Human Genetics (2006) 14,...

This preview shows document pages 1 - 2. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online