The GeWare data warehouse platform for the analysisof molecular-biological and clinical data

We introduce the GeWare data warehouse platform for the integrated analysis of clinical information, microarray data and annotations within large biomedical research studies. Clinical data is obtained from a commercial study management system while publicly available data is integrated using a mediator approach. The platform utilizes a generic approach to manage different types of annotations. We outline the overall architecture of the platform, its implementation as well as the main processing and analysis workflows.

[1]  Jürgen Läuter,et al.  Gene expression analysis reveals evidence for increased expression of cell cycle-associated genes and Gq-protein-protein kinase C signaling in cold thyroid nodules. , 2005, The Journal of clinical endocrinology and metabolism.

[2]  Simon C. Potter,et al.  An overview of Ensembl. , 2004, Genome research.

[3]  Toralf Kirsten,et al.  Interactions in Oligonucleotide Hybrid Duplexes on Microarrays , 2004 .

[4]  P. Stadler,et al.  Sensitivity of Microarray Oligonucleotide Probes: Variability and Effect of Base Composition , 2004 .

[6]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[7]  David Botstein,et al.  The Stanford Microarray Database , 2001, Nucleic Acids Res..

[8]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[9]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[10]  Karen Schlauch,et al.  GeneX: An Open Source gene expression database and integrated tool set , 2001, IBM Syst. J..

[11]  Erhard Rahm,et al.  Flexible Integration of Molecular-Biological Annotation Data: The GenMapper Approach , 2004, EDBT.

[12]  M. Bittner,et al.  Data management and analysis for gene expression arrays , 1998, Nature Genetics.

[13]  H. Döhner,et al.  Matrix‐based comparative genomic hybridization: Biochips to screen for genomic imbalances , 1997, Genes, chromosomes & cancer.

[14]  Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource , 2003 .

[15]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[16]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[17]  S. S. Young,et al.  Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment , 1993 .

[18]  Erhard Rahm,et al.  An Integrated Platform for Analyzing Molecular-Biological Data Within Clinical Studies , 2006, EDBT Workshops.

[19]  R. Spang,et al.  A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling. , 2006, The New England journal of medicine.

[20]  Erhard Rahm,et al.  Comparative Evaluation of Microarray-based Gene Expression Databases , 2003, BTW.

[21]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[22]  Martin Vingron,et al.  Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis , 2002, Bioinform..

[23]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.