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Research Projects

BMBF Project: A Datawarehouse for the reconstruction and analysis of Micro-RNA metabolic network control

Bioinformatics modelling and simulation of biological networks are one of the most important areas in system biology. Biological networks are powerful frameworks to integrate experimental as well as database knowledge in order to model biological interactions and systems. Therefore, different biological networks exist, such as protein-protein-interaction networks, signalling networks, gene-regulation-networks, and metabolic networks, among others. However, the fine- and fast-response regulation mechanisms within cells, like realized by microRNAs, have not been modelled, either simulated due to the lack of biological data.

MicroRNAs are one of the most important mechanisms in the fine-regulation of meany biological processes. Many reports have already shown, that this new ľomic level opens the door to a completely new cell mechanisms. Although, the investigation on microRNAS is still in its beginning, it was possible to demonstrate, how big the impact of microRNA regulation can be. Right now, data about microRNA is very limited and not connected to other ľomic level showing its regulation mechanisms. Therfore, we aim to build a new microRNA database, which can be linked to other life-schience databases in a datawarehouse approach. The aim is to reconstruct microRNA-metabolic networks showing the impact of various microRNA, whoich later on can be simulated.

Therefore, our project partner in Izmir will revise their existing RNA data and made this information accessible in a new relational database. This database will be the base for the modelling, analysis, and reconstruction of the biological networks in Bielefeld. Computer scientists from Bielefeld will integrate the new microRNA database into an existing database called DAWIS-M.D. where it will be semantically connected to other life-science databases, such as KEGG, HPRD, MINT, and IntAct, among others. This will result in biological correlation covering the most important ľomic level.

Once integrated in the datawarehouse, the modelling tool VANESA ( will be extended in its functionality to reconstruct, analyse, and automatically simulated the microRNA-metabolic networks in the Petri net language. Thus, using VANESA scientists will have the possibility to predict complex networks from RNA particles, extend existing networks with RNA fragments, and/or extend already known networks from literature with RNA information. Besides the technical realization of this novel approach, we aim to investigate the microRNA-metabolic networks in the context of our cardiovascular networks, which were reconstructed without microRNA interference in previouse work. Up to now, it was not possible to integrate this new level of micro-RNA fine regulation.

Another goal we aim to realize is the tissue-specific reconstruction of those networks. With additional data from our partners from Izmir it is planned to reconstruct a 3D cell in the software application CellMicrocosmos, showing the regulation range of microRNA. Especially the membrane and nucleous transport is of great interest. With the data from the datawarehouse we are already able to determine the location of many different genes. In combination with the microRNA we will try to show the specific location of regulation and moreover the time of regulation. This will lead to new insights in fundamental research.


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