A bioinformatic and genetic approach to understand gene regulation and dysregulation in breast tumor development and progression
Project leader and key members:
Lars O. Baumbusch and Anne-Lise Børresen-Dale
Home address Internet:
http://radium.no/borresen/?k=borresen/Projects_ALBD&aid=2835
Department/Institute:
Department of Genetics, Institute for Cancer Research
Main aim project:
The aim of this subproject is to
a) establish, evaluate and possibly develop new bioinformatical tools to handle the massive data obtained from microarray experiments to compare gene expression- with gene copy number data from classical and various array based CGH analyses.
b) Identify and characterize genes that are dysregulated by other mechanisms than copy number alterations.
c) Analyze the impact of the above identified genes (or gene clusters) on clinical parameters and patient outcome.
d) Analyze experimentally the role of mRNA binding proteins using CRD-BP and MYC genes as a model system, and search for similar protein motifs and investigate their role in breast tumorigenesis.
Important results:
Microarray-based Comparative Genome Hybridization (array CGH) provides the possibility to connect DNA copy-aberrations with genomic map positions. Different types of arrays may be used in such analyses, cDNA, BAC arrays containing genomic DNA or oligoarrays. In close collaboration with the Institute of Informatics, University of Oslo, UCSF and the Stanford University a comparative study of the different methods is performed based on state-of-the-art statistical modeling and analysis methods.
Lingjærde OC, Baumbusch LO, Liestøl K, Glad I and Børresen-Dale AL CGH-Explorer: a program for visualization and analysis of CGH-array data. Bioinformatics 21(6): 821-822.
Methods:
Equipment:
Collaborators:
Ole Christian Lingjærde and Knut Liestøl, Department of Bioinformatics, University of Oslo, Norway.
Ingrid K. Glad, Department. of Mathematics, University of Oslo, Norway.
Collaborators other countries:
Heike Pospisil, Alexander Herrmann and Jens Reich, Department of Bioinformatics, Max Delbrück Center for Molecular Medicine, Germany.
Jeff Ross, McArdle Laboratory, University of Wisconsin, Madison, USA.
Koei Chin and Joe W. Gray, UCSF Cancer Center, University of California San Francisco, USA.
John R. Pollack, Department of Pathology and Howard Hughes Medical Institute (HHMI), Stanford University, USA.
Patrick O. Brown, Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, USA.
David Botstein, Department of Genetics, Stanford University School of Medicine, USA.
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