PDF file: EURASNET Annual Report 2008

Participant 5A/B – Peer Bork/Rolf Apweilera) Work performed during the period• WP25A. Sharing the source code of tools for identification and display for alternative transcripts.5B. The EBI hosts the Alternative splicing and transcript diversity (ASTD) database.http://www.ebi.ac.uk/astd/The data is publicly available and provides the consortium with a genome wide view of alternative splice eventsand full length transcripts for human, mouse and rat. The ASTD group is happy to incorporate datasets fromconsortium members that are publicly available and for which there is an interest and continued funding tomaintain.Releases 6 & 7 of the ASTD database made a number of improvements in the display of data, speed ofsearching and expansion in the data formats in which data can be exported. New data integration includedexperimental validation of splicing events by RT-PCR from the ATD consortium, miRNA target predictions forHuman and mouse and improvements to the transcript start site (TSS) for these species.• WP45A. User feedback and delivery of the code for displaying alternative splicing events in various datasets5B. The ASTD database is maintained and updated in response to user feedback, data from consortium membersand new publicly available genome wide data.• WP65A. Continuation of the comparative analysis of alternative splicing. Work towards a manuscript on theidentification of an entire network of motifs associated with alternative splicing• WP85A. By comparative analysis of several mammals, all non-coding conserved regions around skipped exonswere analyzed and compared to each other. Furthermore the neighborhood of motifs enriched this way wasanalysed to arrive at significant motifs for alternative splicing, some of them could be validated experimentally.5B. Genome wide splicing factor data generated from this work package can be visualized on the the ASTDweb site• WP165A. Peer Bork talked about approaches to alternative splicing on several conferences.• WP175B. Bioinformatics is increasingly being used to improve our understanding of biology. The massive amount ofinformation and bioinformatics tools must also be interlinked to enhance exploration and biologicallymeaningful interpretation. The EBI is Europe’s main provider of data resources for biologists, also providingtools for searching, retrieving and interpreting the data. The EBI has also a big commitment into “TrainingBioinformatics” and has a tripartite User-Training Programme:One initiative is the roadshow, with more information please see herehttp://www.ebi.ac.uk/training/roadshow/139