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Computational Characterization of Genome-wide DNA-binding Pro les


Rödelsperger,  Christian
Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Rödelsperger, C. (2011). Computational Characterization of Genome-wide DNA-binding Pro les. PhD Thesis, Freie Universität Berlin, Berlin.

The work and data that is presented in this thesis is part of a collaborative project that is funded by the Berlin Center for Regenerative Therapies. A number of people have contributed to this work and for clarity I will now mention the individual contributions. Stefan Mundlos, Peter N. Robinson and Jochen Hecht designed this project with the purpose of studying bone development using ChIP-seq in a chicken model. Jochen Hecht and Asita Stiege established the ChIP-seq protocol and together with Daniel Ibrahim, Hendrikje Hein, and Catrin Janetzky carried out the immunoprecipitations and sequencing. Peter Krawitz was responsible for the data processing that involved base calling and basic quality control. Daniel Ibrahim contributed to the analysis on the Hox proteins identifying the Q317K mutant to be related to Pitx1 and Obox family members. Sebastian Kohler and Sebastian Bauer carried out the computation of the Gene Ontology similarity data and random walk distances that I used for the target gene assignments in chapter 5. The results for the EMSA experiments that are shown in chapter three has been carried out by Asita Stiege. The work on target gene assignment that is presented in chapter 5 has been published in Nucleic Acids Research [1]. All the remaining methods, data and the experimental results will be partially be included in future publications by Ibrahim et al. and Hein et al..