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DIAL Micro Array CGH Database

DIAL Micro Array CGH Database. E.M. Bakker, F.J. Sicking, H.L.A. van der Spek LIACS,Leiden University Niels Bohrweg 1, 2333 CA Leiden {erwin, sicking, hvdspek}@liacs.nl. Abstract Within DIAL , the Data Integration and Logistics project

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DIAL Micro Array CGH Database

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  1. DIAL Micro Array CGH Database E.M. Bakker, F.J. Sicking, H.L.A. van der Spek LIACS,Leiden University Niels Bohrweg 1, 2333 CA Leiden {erwin, sicking, hvdspek}@liacs.nl

  2. Abstract Within DIAL, the Data Integration and Logistics project of the Centre for Medical Systems Biology (CMSB), we developed a secure, reliable, and scalabledatabase solution for the vast amounts of experimental micro array comparative genomic hybridization (CGH) data and images from the different CMSB research groups. The main goals of the new database are data consolidation and data integration. That is, through standard control mechanisms for data quality, data preprocessing, data referencing (BAC), and meta data (CGH MIAME), it is ensured that the stored data represent the original experimental data in an accurate and highly accessible way. Furthermore, the applied standards for normalization, smoothing, and referencing allow multiple experiment integration, and a controlled interface with further analysis and visualization tools.

  3. Groups Involved • Micro Array Core Facility, VUMC: Bauke Ylstra, Jose Luis Costa, Anders Svensson, Paul vden IJssel, • Center for Human and Clinical Genetics, LUMC: Judith Boer, Peter Taschner, and others • Department of Molecular Cell Biology, Laboratory for Cytochemistry and Cytometry: Karoly Szuhai • Leiden University, Leiden Institute of Advanced Computer Science (LIACS)

  4. Micro Array CGH Data Flow (I)

  5. Micro Array CGH Data Flow (II)

  6. Consistent Data Handling - Latest BAC/Clone position tables. - Supports BlueFuse, GenePix, Imagene, with data integrity checks - Generic metadata support ready for MIAME support - Data Quality checks Etc.

  7. Standardized Pre- and Post-Processing- Spot Estimation- Normalization Procedures- Filtering- Smoothing Techniques Etc.

  8. - Perl Programming Interface- SQL Command Line Interface- Query by Selection

  9. VISUAL FEEDBACK • Get immediate visual feedback of your uploaded experiments. • Automatic BAC/Oligo reference file linking. • Use standardized processing like normalization, smoothing, etc. • Sensible default settings supporting data quality and integrity. • And much more …

  10. Easy DAS Server Creation For Integrating your Experimental Data with ENSEMBL

  11. Select and View

  12. Get corresponding RefSeq/Gene information related to your experiment.

  13. Get the original experimental Data in context. Get a detailed GBrowse CGH Profile of your experiment.

  14. DIAL Data Export • SeeGH, Ensembl, Rosetta Resolver, data mining, etc. TIGR MeV:

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