The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
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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In the citing paper
“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]
In the citing paper
“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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Cites
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
Self-citationThe Gene Ontology (GO) database and informatics resource
Gene Ontology Consortium (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,596
Davenport, Y. B., Adland, M. L., Gold, P. W., & Goodwin, F. K. (1984) · The Lancet · doi:10.1016/s0140-6736(84)92810-1 · Cited by 2,925
The Wellcome Trust Case Control Consortium, U.K.
Mossman, K. (2008) · Scientific American · doi:10.1038/scientificamerican0108-42a · Cited by 2,714
A new multipoint method for genome-wide association studies by imputation of genotypes
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
the NIDDK IBD Genetics Consortium, Barrett, J. C., the Belgian-French IBD Consortium, the Wellcome Trust Case Control Consortium, Hansoul, S., Nicolae, D. L., Cho, J. H., Duerr, R. H., Rioux, J. D., Brant, S. R., et al. (2008) · Nature Genetics · doi:10.1038/ng.175 · Cited by 2,593
Replication of Genome-Wide Association Signals in UK Samples Reveals Risk Loci for Type 2 Diabetes
Zeggini, E., Weedon, M. N., Lindgren, C. M., Frayling, T. M., Elliott, K. S., Lango, H., Timpson, N. J., Perry, J. R. B., Rayner, N. W., Freathy, R. M., et al. (2007) · Science · doi:10.1126/science.1142364 · Cited by 2,194
Nyholt, D. R. (2004) · The American Journal of Human Genetics · doi:10.1086/383251 · Cited by 1,699
Walking the Interactome for Prioritization of Candidate Disease Genes
Köhler, S., Bauer, S., Horn, D., & Robinson, P. N. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.02.013 · Cited by 1,268
Cited by
Sorted by citations
Biological insights from 108 schizophrenia-associated genetic loci
Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577
MAGMA: Generalized Gene-Set Analysis of GWAS Data
de Leeuw, C. A., Mooij, J. M., Heskes, T., & Posthuma, D. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004219 · Cited by 3,653
Visscher, P. M., Brown, M. A., McCarthy, M. I., & Yang, J. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.029 · Cited by 2,425
Common variants conferring risk of schizophrenia
†Genetic Risk and Outcome in Psychosis (GROUP), Stefansson, H., Ophoff, R. A., Steinberg, S., Andreassen, O. A., Cichon, S., Rujescu, D., Werge, T., Pietiläinen, O. P. H., Mors, O., et al. (2009) · Nature · doi:10.1038/nature08186 · Cited by 1,677
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013
Wang, J., Duncan, D. T., Shi, Z., & Zhang, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt439 · Cited by 1,512
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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