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NeuroGeM, a knowledgebase of genetic modifiers in neurodegenerative diseases

Dokyun Na15, Mushfiqur Rouf2, Cahir J O’Kane3, David C Rubinsztein4 and Jörg Gsponer1*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, Centre for High-throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada

2 Department of Computer Science, University of British Columbia, 2366 East Mall, Vancouver, BC V6T 1Z4, Canada

3 Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK

4 Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK

5 Present address: School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea

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BMC Medical Genomics 2013, 6:52  doi:10.1186/1755-8794-6-52

Published: 14 November 2013

Abstract

Background

Neurodegenerative diseases (NDs) are characterized by the progressive loss of neurons in the human brain. Although the majority of NDs are sporadic, evidence is accumulating that they have a strong genetic component. Therefore, significant efforts have been made in recent years to not only identify disease-causing genes but also genes that modify the severity of NDs, so-called genetic modifiers. To date there exists no compendium that lists and cross-links genetic modifiers of different NDs.

Description

In order to address this need, we present NeuroGeM, the first comprehensive knowledgebase providing integrated information on genetic modifiers of nine different NDs in the model organisms D. melanogaster, C. elegans, and S. cerevisiae. NeuroGeM cross-links curated genetic modifier information from the different NDs and provides details on experimental conditions used for modifier identification, functional annotations, links to homologous proteins and color-coded protein-protein interaction networks to visualize modifier interactions. We demonstrate how this database can be used to generate new understanding through meta-analysis. For instance, we reveal that the Drosophila genes DnaJ-1, thread, Atx2, and mub are generic modifiers that affect multiple if not all NDs.

Conclusion

As the first compendium of genetic modifiers, NeuroGeM will assist experimental and computational scientists in their search for the pathophysiological mechanisms underlying NDs. http://chibi.ubc.ca/neurogem webcite.

Keywords:
Neurodegenerative diseases; Genetic modifiers; Database; Knowledgebase; Alzheimer’s disease; Parkinson’s disease; Huntington’s disease