Here is the full abstract:

Predicting Functionality of Protein-DNA Interactions by
Integrating Diverse Evidence

Chromatin immunoprecipitation (ChIP-chip) experiments enable
capturing physical interactions between regulatory proteins and DNA
in vivo. However, measurement of chromatin binding alone is not
sufficient to detect regulatory interactions. A detected binding event
may not be biologically relevant, or a known regulatory interaction
might not be observed under the growth conditions tested so-far. To
correctly identify physical interactions between TFs and genes and
to determine their regulatory implications under various experimen-
tal conditions, we integrated ChIP-chip data with motif binding sites,
nucleosome occupancy and mRNA expression datasets within a pro-
babilistic framework. This framework was specifically tailored for the
identification of functional and non-functional DNA binding events.
Using this, we estimate that only 50% of condition specific protein-
DNA binding in budding yeast is functional. We further investigated
the molecular factors determining the functionality of protein-DNA
interactions under diverse growth conditions. Our analysis suggests
that the functionality of binding is highly condition specific and highly
dependent on the presence of specific co-factors. Hence, the joint
analysis of both, functional and non-functional DNA binding may lend
important new insights into transcriptional regulation.

Link to the publication.

Session speakers are Rob Williams, Andrew Su, Eric Schadt and Ritsert Jansen.
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A new EU project, coordinated by Andreas Beyer of the BIOTEC together with the European Project Center of the TU Dresden is starting October 1st, 2008. The EU supports this three year project with almost € 2.5 million. The project “PhenOxiGEn” is addressing the relation of genetic variation and mechanisms that regulate oxidative stress responses of a cell. A cell’s survival depends on its ability to mount a successful stress response when challenged by damages from the environment. In humans, oxidative stress is known to be involved in aging, cancer, atherosclerosis, Alzheimer’s and Parkinson’s disease among others. These diseases are caused by a complex interplay between lifestyle and our individual genomes. Hence, not everybody is equally likely to develop such disease. Many genetic variations associated with complex diseases have been identified in the past. However, we often do not know how these variations affect the genesis of a disease. The projects aim is to extend the knowledge of the genetic factors controlling stress responses. Further partners are Jürg Bähler from the University College London, Christopher Workman from the Technical University of Denmark in Lyngby and Ruedi Aebersold from the ETH Zurich.