PDF file: EURASNET Annual Report 2008

Work Package 4 The Alternative Splicing and TranscriptDiversity (ASTD) DatabaseLead Participant: Rolf Apweilerdeliverables: 132 Improved tools for combined searches and user-friendlyaccess to the ASD database; Integration of additionalspecies to ASTD (continuation of del.7, month 30).154 Fast DB already contains an algorithm that allows analysisof Affymetrix splicearray datafiles. We will create aninterface that allows direct visualization of splicearray datain FAST DB (month 42).155 Integration of an algorithm that computes the likelihood ofsequences to be single stranded (PU) values into FAST DB(month 42).156 The EURASNET member Stamm published a method tocalculate a statistical value (PU value) that expresseswhether a given nucleotide in an RNA is single or doublestranded. Experimental data show that exonic regulatoryelements are preferably in single stranded conformation.We will implement a graphic representation of thisalgorithm in the FAST DB database (Hiller, M., Zhang, Z.,Backofen, R., and Stamm, S. (2007). pre-mRNA secondarystructure and splice site selection. PLOS Genetics 3, 2147-2155) (month 42).monthplanned achieved30 3042 3642 on target42 42Objectives of the work package• To maintain, update and expand the alternative splicing database (ASD) hosted at the EBI.Short description of activities132 Improved tools for combined searches and user-friendly access.The content of ASD (alternative splicing database) and ASTD (Alternative Splicing and Transcript Diversity database) havebeen combined and were integrated into the integrate database (i8). To facilitate information retrieval and to make thedatabase more user-friendly, the database has integrated human and mouse miRNA targets prediction, has an improvedadvanced search field and an improved display of splicing events for each gene. Splicing events are visualized with otherinformation, such as reading frames, miRNA targets, transcriptional start sites, protein coding regions, lists of verifiedtranscripts, polyA sites, and cDNA libraries used to clone the events. Furthermore, specific events can be identified by anadvanced search field featuring: chromosomes, splicing type, gene ontology and transcript in silico expression. Finally,splicing Junction Array expression data for Mus Musculus from a study on the functional coordination of alternative splicingin the central nervous system were integrated. The database is at http://www.ebi.ac.uk/astd/main.html154 Create an interface that allows direct visualization of splicearray data.Affymetrix data have been integrated into FAST DB. Currently, this integration is seen by EURASNET members that useAffymetrix arrays and have the analysis done by Pierre de LaGrange, a previous member of the group of EURASNETmember Didier Auboeuf.155 Integration of an algorithm that computes the likelihood of sequences to be single stranded.D155 can be see at http://www.fast-db.com/fastdb2/frame.html156 Implement a graphic representation of the Stamm algorithm in the FAST DB database.D156 is under way and will be implemented by month 42Problems and explanations for delays, postponements etc.##28