NGFN-TRANSFER
Bioinformatics
| Coordinator: | Dr. Ralf Herwig | |
| Institution: | Max Planck Institut für molekulare Genetik, Berlin | |
| Homepage: | www.molgen.mpg.de/~lh_bioinf |
The NGFN-transfer project utilized new methods of proteomics, metabolomics, genotyping and peptide analysis for the identification of mediators and their modes of action that are responsible for the elevated incidence of cardiovascular diseases in patients that suffer from chronic renal failure.
In the subproject „Bioinformatics“ we conducted the analysis, interpretation and integration of the project data:
1. A data integration system was developed that is able to integrate heterogeneous and complex data. The system was used for data exchange and as a collaboration platform for the consortium throughout the project duration [2].
2. A major project goal was the identification of new uremic toxins with molecular networks. An important step towards this goal was the development of new algorithms for network analysis with complex data [3]. In particular, knowledge on molecular pathways that are affected by uremic toxins was rather sparse. We developed a new method that allows combining heterogeneous data and mapping it onto biochemical pathways. This method was implemented as a web server within the IMPaLA system [4]. In total, 129 potential new uremic toxins could be identified. Selected candidates were further experimentally validated [1].
3. We developed a knowledgebase that collects the entire information on the molecular entities and their relations and built a software prototype for practical applications.
Selected publications:
[1] Jankowski V, Schulz A, Kretschmer A, Mischak H, van der Giet M, Schuchardt M, Nierhaus M, Janke D, Herwig R, Zidek W, Jankowski J (2013) The enzymatic activity of the VEGFR2-receptor for the biosynthesis of dinucleoside polyphosphates. J Mol Med, in press. doi:10.1007/s00109-013-1036-y
[2] Dreher F, Kreitler T, Hardt C, Kamburov A, Yildirimman R, Schellander K, Lehrach H, Lange BMH, Herwig R (2012) DIPSBC - Data Integration Platform for Systems Biology Collaborations. BMC Bioinformatics, 13:85. (highly accessed)
[3] Thormann A, Rasche A (2011) Functional Context Network of T2DM. In: Medical
Complications of Type 2 Diabetes (Ed. C. Croniger), pp 213-230. In Tech Publishing ISBN 978-953-307-363-7.
[4] Kamburov A, Cavill R, Ebbels TMD, Herwig R, Keun HC (2011) Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics, 27(20):2917-2918.
IMPaLA system for network analysis of heterogeneous data: impala.molgen.mpg.de
Data integration system software: dipsbc.molgen.mpg.de
Further Coordinators:
In the subproject „Bioinformatics“ we conducted the analysis, interpretation and integration of the project data:
1. A data integration system was developed that is able to integrate heterogeneous and complex data. The system was used for data exchange and as a collaboration platform for the consortium throughout the project duration [2].
2. A major project goal was the identification of new uremic toxins with molecular networks. An important step towards this goal was the development of new algorithms for network analysis with complex data [3]. In particular, knowledge on molecular pathways that are affected by uremic toxins was rather sparse. We developed a new method that allows combining heterogeneous data and mapping it onto biochemical pathways. This method was implemented as a web server within the IMPaLA system [4]. In total, 129 potential new uremic toxins could be identified. Selected candidates were further experimentally validated [1].
3. We developed a knowledgebase that collects the entire information on the molecular entities and their relations and built a software prototype for practical applications.
Selected publications:
[1] Jankowski V, Schulz A, Kretschmer A, Mischak H, van der Giet M, Schuchardt M, Nierhaus M, Janke D, Herwig R, Zidek W, Jankowski J (2013) The enzymatic activity of the VEGFR2-receptor for the biosynthesis of dinucleoside polyphosphates. J Mol Med, in press. doi:10.1007/s00109-013-1036-y
[2] Dreher F, Kreitler T, Hardt C, Kamburov A, Yildirimman R, Schellander K, Lehrach H, Lange BMH, Herwig R (2012) DIPSBC - Data Integration Platform for Systems Biology Collaborations. BMC Bioinformatics, 13:85. (highly accessed)
[3] Thormann A, Rasche A (2011) Functional Context Network of T2DM. In: Medical
Complications of Type 2 Diabetes (Ed. C. Croniger), pp 213-230. In Tech Publishing ISBN 978-953-307-363-7.
[4] Kamburov A, Cavill R, Ebbels TMD, Herwig R, Keun HC (2011) Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics, 27(20):2917-2918.
IMPaLA system for network analysis of heterogeneous data: impala.molgen.mpg.de
Data integration system software: dipsbc.molgen.mpg.de
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