Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Erik van Nimwegen, Core Program Computational and Systems Biology Biozentrum, University of Basel, Switzerland

Title: Inferring transcription regulatory networks using deep sequencing data

Time: Wed, Feb 3, 2010, 4:00pm

Place: MPI für Molekulare Pflanzenphysiologie, Central Building, 1st Floor, Seminar Room

Abstract:
I will discuss an integrated computational approach, called motif activity response analysis (MARA), for reconstructing transcription regulatory networks from genome-wide expression data. Using deep sequencing of 5'ends of mRNAs (deepCAGE) across a variety of tissues in human and mouse we have constructed hierarchical 'promoteromes' of transcription start sites, co-expressed local TSS clusters, and TSS regions.

Starting from these promoteromes we applied probabilistic comparative genomic methods to comprehensively predict functional transcription factor binding sites in all proximal promoter regions of the human and mouse genome. MARA models genome-wide gene expression profiles in terms of these predicted regulatory sites and I will describe how MARA identifies, for a given system of study, the key regulators driving expression changes, their activity profiles across the samples, and the sets of target promoters of each regulator.

I will in particular illustrate the results of the approach on time course data from differentiating human cell lines.

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Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


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