GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases

BMC Genomics

Research Article

Sipko van Dam¹  Rui Cordeiro¹  João Pedro de Magalhães¹  Thomas Craig¹  Shona H Wood¹  Jesse van Dam² 

[1] Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK;Laboratory of Systems and Synthetic Biology, Wageningen University, 6703 HB, Wageningen, Netherlands;

关键词: Aging;    Cancer;    Functional genomics;    Mitochondrial disease;    Network biology;   

DOI  :  10.1186/1471-2164-13-535

 received in 2012-03-21, accepted in 2012-08-22,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundAlthough many diseases have been well characterized at the molecular level, the underlying mechanisms are often unknown. Nearly half of all human genes remain poorly studied, yet these genes may contribute to a number of disease processes. Genes involved in common biological processes and diseases are often co-expressed. Using known disease-associated genes in a co-expression analysis may help identify and prioritize novel candidate genes for further study.ResultsWe have created an online tool, called GeneFriends, which identifies co-expressed genes in over 1,000 mouse microarray datasets. GeneFriends can be used to assign putative functions to poorly studied genes. Using a seed list of disease-associated genes and a guilt-by-association method, GeneFriends allows users to quickly identify novel genes and transcription factors associated with a disease or process. We tested GeneFriends using seed lists for aging, cancer, and mitochondrial complex I disease. We identified several candidate genes that have previously been predicted as relevant targets. Some of the genes identified are already being tested in clinical trials, indicating the effectiveness of this approach. Co-expressed transcription factors were investigated, identifying C/ebp genes as candidate regulators of aging. Furthermore, several novel candidate genes, that may be suitable for experimental or clinical follow-up, were identified. Two of the novel candidates of unknown function that were co-expressed with cancer-associated genes were selected for experimental validation. Knock-down of their human homologs (C1ORF112 and C12ORF48) in HeLa cells slowed growth, indicating that these genes of unknown function, identified by GeneFriends, may be involved in cancer.ConclusionsGeneFriends is a resource for biologists to identify and prioritize novel candidate genes involved in biological processes and complex diseases. It is an intuitive online resource that will help drive experimentation. GeneFriends is available online at: http://genefriends.org/.

【 授权许可】

Unknown   
© van Dam et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.