Transcript Document

Oryza group
Arjan, Claire, Robert & Ruud
Case study: Saccharomyces cerevisiae grown under two different conditions
RNAseq data plataform: Illumina
Goal: Generate a platform where the user will input files and directory
names, make the choice for trimmed or untrimmed RNAseq data to be
assembled, and retrieve the top 100 expressed genes provided with
biological information.
Bioinformatics tools aimed to be used: TopHat, samtools, cufflinks, perl
scripts, cytoscape
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RNAseq
data
Trimmed
Untrimmed
TopHat
Cufflinks
Pick up the 100 most highly
expressed genes in the yeast
RNAseq
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Progress:
•
Arjan: Developed a package to retrieve gene
sequences.
•
Claire: Correlation between GC content and gene
expression.
•
Robert: Trimming, Length sorting, TopHat,
Cufflinks, retrieving Top100, formatting pipeline.
•
Ruud: Correlation between exon/intron size and
gene expression. Generate output table.
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Biological questions on the selected genes:
•
Correlation between exon/intron size and gene
expression
•
Correlation between GC content and gene
expression
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Using conserved palindrome motif list in
yeast:
1.
2.
Look for proportion of G/C-only
repeats in top 100 gene list?
Look for repeats length in top 100
gene list?
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... compare results with profile of less expressed genes?
... compare differently expressed genes on both growth
conditions?
... GO annotation? Plot data on cytoscape?
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Next week packages:
•
Arjan: Codon usage over Top100 genes.
•
Claire: Correlation between conserved palindrome
sequences and gene expression.
•
Robert: GO-annotation package.
•
Ruud: retrieve Top100 gene information from
NCBI.