Public%20data%20-%20available%20for%20projects

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.stjudere
  search.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 (1500)
• Deadline for problem formulation
• hand-in 1/2 page