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Populus

Populus. Petra van Berkel Casper Gerritsen Astri Herlino Brian Lavrijssen. Dataset and goal. Dataset Organism of choice is S. cerevisiae 2 conditions (batch & chemostat ) Response to glucose limitation 3 replicates per condition Goal Find differentially expressed genes

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Populus

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  1. Populus Petra van Berkel Casper Gerritsen AstriHerlino Brian Lavrijssen

  2. Dataset and goal • Dataset • Organism of choice is S. cerevisiae • 2 conditions (batch & chemostat) • Response to glucose limitation • 3 replicates per condition • Goal • Find differentially expressed genes • Define gene functions • Find a correlation between gene expression and transcript properties

  3. Pipeline functionality (M) • Generate differential expression data • TopHat, Cufflinks, Cuffmerge and Cuffdiff (B)  • Extract all significant differentially expressed genes (P) • Default settings  • Changed q-value (<1e-5) (→ literature)  • Top up- and downregulated genes  • Find GO-terms for selected up- and downregulatedgenes (A) 

  4. Pipeline functionality (S) • Create a volcano plot & scattered plot (B)  • Perform GO-enrichment (A)  • Create graphs • Find correlation between gene expression and transcript properties (C) • GC-content • Transcript length • Codon usage • Intron length

  5. Pipeline functionality (C) • Visualize highly expressed genes in interaction network (P) • Create a summary (B) • Find pathway information for up- and downregulatedgenes (KEGG)

  6. Issues/challenges • Find modules of co-expressed genes • Need > 4 different conditions • Validation of all output • Writing rapport

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