Open analysis

You will use the genes that are differentially expressed in response to oxidative stress in the yeast Saccharomyces cerevisiae .
Lucau-Danila A, Lelandais G, Kozovska Z, Tanty V, Delaveau T, Devaux F, Jacq C Early expression of yeast genes affected by chemical stress Mol Cell Biol. 2005 Mar;25(5):1860-8 PDF
You are expected to :

• retrieve the upstream sequences
• discover significant motifs (do not hesitate to use different k-mer lengths !) within all the genes differentially expressed at 20 min
• predict up to 2 factor(s) which binding specificity correspond to discovered motif(s)
• locate the putative binding sites on the 3 clusters of genes
• perform the appropriate negative controls

List of files:

• dataFile_timeCourse_filteredGenes.txt comprising the microarray results only for genes differentially expressed at 20 minutes.
• cluster1: early cluster2:middle cluster3:late plot Clustering of the same genes into 3 clusters (K-means euclidian distance)
• genes that are not differentially expressed

To select a list of 10 binding sites that are the most promising (i.e. most likely to be true and that you will give to your colleagues to test experimentally):

• get external information on these factors, does it make sense in the studied biological context ?
• you have at your disposal ChIP-seq data for the factor Pdr1p in S. cerevisiae (published in 2014 PDF) in BAM format. You may search the peaks and visualize them in the genome browser to help you identify the potential binding sites. Note that the ChIP-seq was not performed in stress conditions.
• location of bam files: /genomic/ue_m2_cisreg