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Advanced Bioinformatics. Group Medicago Basic Project: Gene expression in yeast. Members. Jente Ottenburghs Lifei Li Yuebang Yin Nick Brouwers. Objectives. Make a top 100 of the most highly expressed genes Find correlations between gene expression & transcripts GC content
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Advanced Bioinformatics Group Medicago Basic Project: Gene expression in yeast
Members • JenteOttenburghs • Lifei Li • Yuebang Yin • Nick Brouwers
Objectives • Make a top 100 of the most highly expressed genes • Find correlations between gene expression & transcripts • GC content • Transcript length • Intron length • Codon usage • (optional) Visualization of an interaction network Make use of Tophat, Cufflinks, perl etc.
Steps • Run Tophat • Use Tophat output as Cufflinks input • Use Cufflinks output to build Perl scripts • Show our analysis and hopefully visualization
Plan: Data gathering • Create output with Cufflinks • Build Fasta from transcripts.gtf and genome.fa(all) • Vizualize interaction networks (Yuebang) • Build scripts to: • analyse our Fasta, GC content, length etc. (Nick) • implement gene expression (Lifei Nick) • sort gene expression (Lifei and Nick) • show intron length (all together) • determine condonusage (Jente)
