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Extending XMLPipeDB to create GenMAPP‐compatible gene databases for the analysis of DNA microarray data from human pathogens
Author(s) -
Parks Kelly C,
Hirning Andrew J,
McDonald Kelia,
Dionisio John David N.,
Dahlquist Kam D
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.669.2
Subject(s) - ensembl , database , computer science , uniprot , sql , relational database , microarray databases , xml , biological database , information retrieval , gene , dna microarray , biology , bioinformatics , genomics , world wide web , genome , genetics , gene expression
The GenMAPP suite is a powerful tool for viewing and analyzing DNA microarray data on biological pathways and performing Gene Ontology term over‐representation analysis. However, the use of GenMAPP and MAPPFinder is limited to those species for which a GenMAPP‐compatible Gene Database exists. Currently, these Gene Databases are based on Ensembl, which is limited to (mostly) animal species. Furthermore, the process of creating a Gene Database is sensitive to changes in flat file formats. To extend the use of GenMAPP for plants and microorganisms, and to create a method for database creation that was robust to changes in file formats, we created XMLPipeDB, an open source tool chain for building relational databases from XML sources. The tool chain reads an XSD and automatically generates an SQL schema, Java classes, and Hibernate mappings. It also provides functionality for database configuration, importing data, performing queries, and exporting GenMAPP‐compatible Gene Databases based on data from UniProt and Gene Ontology. We used XMLPipeDB to update the Gene Database for Saccharomyces cerevisiae and create new ones for Mycobacterium tuberculosis , Pseudomonas aerugenosa , and Staphylococcus aureus . We have used our new Gene Databases to analyze previously published DNA microarray data for each of these organisms, generating new findings that were not previously reported.