1. Transcriptomics: GeneSpring/EST integration Joe Wood

2. Transcriptomics on Bio-Linux ● GeneSpring ● EST pipeline ● Maxd ● MIAME data standards

3. GeneSpring ● Silicon Genetics ● Installed on Bio-Linux ● Licences available for EG grant holders ● GeNet Database ● MIAME compliant

4. GeneSpring Features ● Data normalisation ● Data clustering ● 3D visualisation ● Pathway views ● Expression profile comparison ● Scripting ● Advanced statistical tools

5. Data Normalisation

6. Data clustering

7. 3D Visualisation

8. Expression Profile Comparison

9. Pathway Views

10. Advanced Statistical Tools

11. Scripting

12. EST pipeline ● EGTDC Edinburgh ● Installed on Bio-Linux ● Raw sequence files (ABI,SCF) ● Fasta files ● DbEST-ready submission files

13. Trace2dbest.pl ● Base-calling -PHRED ● Vector trimming - Cross_Match ● PolyA tail trimming ● Low-quality sequence trimming ● Optional BLAST annotation ● DbEST submission file ● Fasta file

14. Integrating GeneSpring/EST ● GeneSpring 'genomes' ● GeneSpider automatically annotates ● GeneTable files ● Can create own GeneTables ● EST annotations, other lab-specific annotations

15. Local Data Analysis EGTDC Public Raw Data maxdView Maxd database GeneSpring Maxd Database GeNet Database GEO Array Express Bio-Linux