Integration of J-Express with ArrayExpress

1. Partner 20 University of Bergen Inge Jonassen - inge@ii.uib.no Kjell Petersen - kjellp@ii.uib.no Integration of J-Express with ArrayExpress

2. Introduction • Role in DESPRAD/TEMBLOR project • Integration of analysis tool J-Express with ArrayExpress • New analysis methods – exploiting integration • Population of database • Dissemination • Norwegian Microarray Consortium • Cooperation to establish and make available microarray technology in Norway • Bioinformatics solutions and support

3. Design for an integrated system –solution for Norwegian Microarray Consortium Image analysis software, e.g. GenePix Scanner J-Express User BASE ArrayExpress Goals:- ensure efficient, reliable data handling- comply with standards- integration

4. J-Express • A fully integrated tool for processing and exploring microarray data • Graphical user interface, fully portable (Java) • Powerful but intuitive and simple user interface • Produces high quality (vector) graphics and full documentation of all steps (meta-data) • “Figure and caption for publication” • Project management system • Fully supportive of MAGE-ML standard – both for import and export • Integration with databases and other tools using MAGE-ML or MAGE objects

5. Project management window Expression profiles of selected data set Meta data Analysis windows

6. Array Express Submit <MAGE-ML> <AuditAndSecurity_package> < > </ > </ > < > < > </ > </ > < > </ > </MAGE-ML Download <MAGE-ML> <AuditAndSecurity_package> < > </ > </ > < > < > </ > </ > < > </ > </MAGE-ML <MAGE-ML> <AuditAndSecurity_package> < > </ > </ > < > < > </ > </ > < > </ > </MAGE-ML MAGE-ML stream Query Retrieval Import BASE MAGE-OM Export Java MAGEstk based MAGE Java framework J-Express core J-Express core J-Express core J-Express core J-Express core

7. MAGE Java framework cont. • MAGE-ML import to J-Express • Single or several files • MAGE-ML export from J-Express • Prototype for export of filtered, normalized and clustered data. • Soon to be extended for analysis done in JE's new module for batch pipeline import of raw data. • URL query for retrieval at object level (instead of whole experiments)

8. data process Protocol Application Protocol Software Application Software Parameter Parameter Value Parameter Parameter Value Parameter Parameter Value Description Values MAGE-ML export – processes Transformation

9. Transformation Transformation BioAssayData BioAssayData BioAssayData BioAssayData Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension Dimension BioDataCube BioDataCube BioDataCube Data in text file Data in text file Data in text file MAGE-ML export – data BioAssayData

10. Helping to populate ArrayExpress • Upgrading and maintenance of BASE 1.2.x installation • User training • Internal courses/workshops • Norwegian Microarray Consortium courses • Contribute to MAGE-ML export from BASE • KP registered for BASE meeting in Lund November 5th 2003. • Vegard Nygaard (NMC partner in Oslo) • Nicklas Nordborg (Main developer of BASE 2.0). • Participation in “MAGE jamboree” at EBI Dec 2003

11. J-Express – progress • Reworked Meta-Data module • Suite of tools for quality control of arrays and batch pipeline import (merging of replicates, filters, normalisation etc) • Additional features • Feature Subset Selection • Class Predictor • Cross Validation • New and improved imputation technique

12. J-Express cont. • Data with reliability estimates • Fundamental extension in J-Express • Several sources for reliability estimates • Error-model • Initialised with error parameters from spot finding program result files (e.g. GPR) or MAGE-ML files. • MAGE-ML directly • Replicates

13. People involved • Bjarte Dysvik – Main developer of J-Express • Trond H. Bø – FSS, Statistics • Ugis Sarkans, Helen Parkinson, Alvis Brazma – Array Express • Svenn Grindhaug, Vegard Nygård, Nicklas Nordborg - BASE • Inge Jonassen • Kjell Petersen