1. Public data - available for projects 6 data sets: –Human Tissues –Leukemia –Spike-in –FARO compendium – Yeast Cell Cycle –Yeast Rosetta Find one yourself !?

2. Human Tissue Atlas 79 human tissues (in duplicates) Among the tissues are: –brain samples –heart and liver samples –fetal samples 22215 probe sets (HGU133A subset) Preprocessed data: –normalized –expression index calculated Used for investigation of global trends and chromosomal organization of transcription, evaluation of gene prediction Su et al., 2004 http://symatlas.gnf.org/SymAtlas/

3. Leukemia Data 43 T-cell ALL arrays with a subset of 35 patients treated with two different treatments ending up in: 1. Relapses: 9 in total –6 -Heme relapse –1 -2nd AML –2 -Other relapses 2. Recovered: 26 Platform: Affymetrix HGU133A Dataset has previously been used for classification problems For more information: Yeoh et al, Cancer Cell, 2002 http://www.stjuderesearch.org/data/ALL1/

4. Spike In Dataset Subset of the SPIKE-IN HGU95 Latin square data "Normal" sample + spike-in of transcripts that hybridize to 14 probe sets (The concentrations of the spike-in is known) 2 series of concentrations: Each probe set is spiked in, in two different concentrations (pM). 12 replicates for each series - four replicates on three GeneChip batches (24 GeneChip CEL files are available in total) Previous usage: a benchmark data set for preprocessing methods

5. FARO compendium Gene expression signatures from 242 experimental factors –From 1700 Affymetrix ATH1 GeneChips Gene expression signature: List of significantly differentially expressed genes Factors addressed: all public data (ATH1, Arabidopsis, 2007) Mutants, stress, chemical, hormonal, tissue. Etc. Organism: Arabidopsis thaliana Data has been processed, available data is: Ranked gene lists for 242 factors Fold changes

6. Yeast Cell Cycle Data The experiment: –Three time-series, where samples were taken from a synchronized yeast cell culture as it progresses through the cell cycle. –Three different synchronization methods to arrest the cell cycle: Two temperature sensitive mutant strains (Cdc15 and Cdc28) that cannot pass the cell cycle at high temperature –Rapid removal of mating factor alpha from the culture, which releases it from arrest. Aim of the original studies: –to determine the genes that fluctuate in expression during the cell cycle –to characterize when in the cell cycle these genes are expressed and repressed. The data set: –three separate files, normalized and preprocessed data.

7. Yeast Rosetta Compendium Dataset consisting of a compendium of expression profiles: –276 deletion mutants (69 of which where unknown at the time) –11 tetracycline-regulatable essential genes –13 compound treatments Data: –P-values and logratios –generated by comparison with 63 control experiments. Data originally used for identifying gene clusters and profiling of unknown ORFs and drug targets. For more information: Hughes et al., Cell, 2000

8. Data Set Overview 242 experiments Rank Fold Change FARO

9. Practical stuff Where: http://www.cbs.dtu.dk/chipcourse/Data.sets/ When: Thursday January 10th Data set discussion 1 (Human tissue, Spike-in, Cell cycle) Monday January 14th Data set discussion 2 (Leukemia, FARO compendium, Rosetta compendium) Wednesday January 16th (15:00) Deadline for problem formulation hand-in 1/2 page