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: Sebastian Proost, MPI-MP, AG Balazadeh

Title: An Ensemble Approach to Dissect Plant Regulatory Sequences * Bioinformatics Affinity Seminar

Time: Wed, Mar 6, 2013, 10am

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
Given recent advances in sequencing technology, acquiring a catalog of all expressed genes is becoming increasingly easy. However, determining the regulatory networks that drive gene expression, in different physiological, developmental or environmental conditions, is to date still a laborious task. Essential for elucidating such gene regulatory networks is the detection of functional cis-acting elements, such as transcription factor binding sites, in the vicinity of expressed genes.
The availability of full genome sequences allows upstream regions of co-expressed genes to be mined for reoccurring motifs, which are likely to be bound by proteins; therefore various tools have been developed to find cis-regulatory elements based on overrepresentation of motifs. We have evaluated the performance of three recently published tools (MEMESuite, MotifSuite and DECOD) on plant data. In line with previous findings, each tool predicts a complementary set of regulatory motifs.
Based on these findings, an automated workflow was developed, which makes use of a combination of these tools to improve detection of putative cis-regulatory elements. Furthermore, using comparative genomics, the phylogenetic conservation of the found motifs is evaluated. Finally, the merits of this workflow are shown on plant datasets.

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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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