Transcriptomics: GeneSpring/EST integration Joe Wood.

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Presentation transcript:

Transcriptomics: GeneSpring/EST integration Joe Wood

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

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

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

Data Normalisation

Data clustering

3D Visualisation

Expression Profile Comparison

Pathway Views

Advanced Statistical Tools

Scripting

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

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

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

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

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