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Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder
Open accessAbstract
We present a method for testing overrepresentation of biological pathways, indexed by gene-ontology terms, in lists of significant SNPs from genome-wide association studies. This method corrects for linkage disequilibrium between SNPs, variable gene size, and multiple testing of nonindependent pathways. The method was applied to the Wellcome Trust Case-Control Consortium Crohn disease (CD) data set. At a general level, the biological basis of CD is relatively well known for a complex genetic trait, and it thus acted as a test of the method. The method, known as ALIGATOR (Association LIst Go AnnoTatOR), successfully detected biological pathways implicated in CD. The method was also applied to a meta-analysis of bipolar disorder, and it implicated the modulation of transcription and cellular activity, including that which occurs via hormonal action, as an important player in pathogenesis.
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“Analyses of bipolar disorder provided evidence of association with hormone action and adherens junctions7,9,10”
From Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways (2015) · cites this paper as [9]
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“INRICH45, ALIGATOR9 and MAGENTA46 are “best SNP per gene” methods that count the number of genes in a pathway where a number of independent SNPs exceed a predefined significance, and adjust for LD and genomic structure with corrected statistics derived by Monte-Carlo simulation.”
From Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways (2015) · cites this paper as [9]
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Granka, J. M., Henn, B. M., Gignoux, C. R., Kidd, J. M., Bustamante, C. D., & Feldman, M. W. (2012) · Genetics · doi:10.1534/genetics.112.144071 · Cited by 81
Genetic Relationship between Schizophrenia and Nicotine Dependence
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Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2
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Fatemifar, G., Hoggart, C. J., Paternoster, L., Kemp, J. P., Prokopenko, I., Horikoshi, M., Wright, V., Tobias, J. H., Richmond, S., Zhurov, A. I., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt231 · Cited by 79
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Whole genome association scan for genetic polymorphisms influencing information processing speed
Michelle Luciano, A., Hansell, N. K., Lahti, J. M. T., Davies, G., Medland, S. E., Räikkönen, K., Tenesa, A., Widén, E., McGhee, K. A., Palotie, A. V., et al. (2010) · Biological Psychology · doi:10.1016/j.biopsycho.2010.11.008 · Cited by 78
From SNPs to Genes: Disease Association at the Gene Level
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REVIEW: Genome‐Wide Findings in Schizophrenia and the Role of Gene–Environment Interplay
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A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin
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“Association List GO Annotator (ALIGATOR) was used to perform analysis of the nonpruned GWAS data as described previously with a few changes (Holmans et al., 2009).”
MethodSelf-citationRitchie, M. D. (2010) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2010.00630.x · Cited by 76
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AKAPs integrate genetic findings for autism spectrum disorders
Poelmans, G., Franke, B., Pauls, D. L., Glennon, J. C., & Buitelaar, J. K. (2013) · Translational Psychiatry · doi:10.1038/tp.2013.48 · Cited by 76
Metadata
- Authors
- Holmans, P., Green, E. K., Pahwa, J. S., Ferreira, M. A. R., Purcell, S. M., Sklar, P., Owen, M. J., O'Donovan, M. C., & Craddock, N.
- Affiliations
- Cardiff University (GB)
- Broad Institute (US)
- Corresponding author
- Holmans, Peter
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2009-07
- Volume
- 85
- Issue
- 1
- Pages
- 13-24
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC2706963
- OpenAlex
- W1991160835
- Cited by
- 378
- References
- 45
- Citations by year
- 2025: 1 · 2024: 2 · 2023: 8 · 2022: 4 · 2021: 12 · 2020: 19 · 2019: 16 · 2018: 18 · 2017: 17 · 2016: 28 · 2015: 34 · 2014: 34 · 2013: 38 · 2012: 52
- FWCI
- 19.44
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
- Keywords
- Gene Ontology, genome-wide association study, single nucleotide polymorphisms, multiple testing correction, Crohn's disease, bipolar disorder, transcriptional regulation, hormone signaling, pathogenesis
- MeSH terms
- Bipolar Disorder, Crohn Disease, Humans, Computational Biology, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Databases, Genetic, Genome-Wide Association Study
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