Article |
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists
BioMedical Informatics Laboratory, Bioengineering Department Politecnico di Milano, I-20133 Milano, Italy
*To whom correspondence should be addressed. Tel: +39 02 2399 3336/3303; Fax: +39 02 2399 3360; Email: masseroli{at}biomed.polimi.it
Received February 14, 2005. Revised April 1, 2005. Accepted April 1, 2005.
Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for computational genome-wise analyses. We developed and made available through GFINDer web server an original approach for the analysis of genetic disorder related genes by exploiting the information on genetic diseases and their clinical phenotypes present in textual form within the Online Mendelian Inheritance in Man (OMIM) database. Because several synonyms for the same name and different names for overlapping concepts are often used in OMIM, we first normalized phenotype location descriptions reducing them to a list of unique controlled terms representing phenotype location categories. Then, we hierarchically structured them and the correspondent genetic diseases according to their topology and granularity of description, respectively. Thus, in GFINDer we could implement specific Genetic Disorders modules for the analysis of these structured data. Such modules allow to automatically annotate user-classified gene lists with updated disease and clinical information, classify them according to the genetic syndrome and the phenotypic location categories, and statistically identify the most relevant categories in each gene class. GFINDer is available for non-profit use at http://www.bioinformatics.polimi.it/GFINDer/.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Yilmaz, P. Jonveaux, C. Bicep, L. Pierron, M. Smail-Tabbone, and M.D. Devignes Gene-disease relationship discovery based on model-driven data integration and database view definition Bioinformatics, January 15, 2009; 25(2): 230 - 236. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Al-Shahrour, J. Carbonell, P. Minguez, S. Goetz, A. Conesa, J. Tarraga, I. Medina, E. Alloza, D. Montaner, and J. Dopazo Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments Nucleic Acids Res., July 1, 2008; 36(suppl_2): W341 - W346. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. W. Huang, B. T. Sherman, Q. Tan, J. Kir, D. Liu, D. Bryant, Y. Guo, R. Stephens, M. W. Baseler, H. C. Lane, et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists Nucleic Acids Res., July 13, 2007; 35(suppl_2): W169 - W175. [Abstract] [Full Text] [PDF]
|
|