Area Chair:

1
Transcriptomics

• Area Chair
• Martin VingronMax-Planck-Institute for Molecular
  Genetics, Berlin, Germany
• Presentation
• Thomas Lengauer
• Max-Planck-Institute for Informatics, Saarbücken,
  Germany

2
Transcriptomics Study of transcriptional
products

• Determination of mRNA levels, i.e. expression
  profiling
• Gene structure, alternative splicing
• Utilization of expression profiles for study of
  biological mechanisms, disease mechanisms
• Application of DNA arrays in chromatin immuno
  precipitation gene regulation

3
Technologies I

• Tagging the mRNA ESTs, SAGE
• Quantitative PCR

4
Technologies II Array based

• cDNA arrays, long oligo arrays immobilize a
  piece of DNA per gene. These are (usually)
  2-color arrays, i.e. two samples are labeled with
  different dyes and hybridized
• Short oligo arrays (Affymetrix) immobilize
  several short oligonucleotides per gene. These
  are 1-color arrays, i.e. one sample is hybridized
  at a time
• Tiling arrays spots do not correspond to genes.
  Instead representative sequences for whole
  genomic regions are spotted

5
Questions I

• Experimental design How to get the most
  information out of the least number of
  hybridizations?
• - Paper by Woo et al Experimental Design for
  Three-Color and Four-Color Gene Expression
  Microarrays

6
Questions II

• What is the product of transcription?
• Gene structure and alternative splicing Paper by
  Cline et al A Statistical Method for Detecting
  Splice Variants from Expression Data
• Tiling arrays Originally used for unbiased
  detection of transcription. Now being used for
  identifying transcription factor binding sites,
  see paper by Li et al A Hidden Markov Model for
  Analyzing ChIP-chip Experiments on Genome Tiling
  Arrays and its Application to p53 Binding
  Sequences

7
Questions III

• Use expression profiles to characterize, e.g.,
• Developmental states
• Disease states
• Leads to classification problem Paper by Soukup
  et al Robust Classification Modeling on
  Microarray Data Using Misclassification Penalized
  Posterior

8
Questions IV

• Common change common regulation?
• Clustering, coexpression Paper by by Dueck et
  al Multi-way clustering of Microarray Data using
  Probabilistic Sparse Matrix Factorization
• Is coexpression mediated by the same
  transcription factor? Compare also paper on
  regulation by Li et al