Prioritization of Candidate Genes for Attention Deficit Hyperactivity Disorder by Computational Analysis of Multiple Data Sources

Overview

Journal Protein Cell

Publisher Oxford University Press

Specialties Biochemistry
Cell Biology

Date 2012 Jul 10

PMID 22773342

Citations 3

Authors

Suhua Chang

Weina Zhang

Lei Gao

Jing Wang

Affiliations

Soon will be listed here.

Abstract

Attention deficit hyperactivity disorder (ADHD) is a common, highly heritable psychiatric disorder characterized by hyperactivity, inattention and increased impulsivity. In recent years, a large number of genetic studies for ADHD have been published and related genetic data has been accumulated dramatically. To provide researchers a comprehensive ADHD genetic resource, we previously developed the first genetic database for ADHD (ADHDgene). The abundant genetic data provides novel candidates for further study. Meanwhile, it also brings new challenge for selecting promising candidate genes for replication and verification research. In this study, we surveyed the computational tools for candidate gene prioritization and selected five tools, which integrate multiple data sources for gene prioritization, to prioritize ADHD candidate genes in ADHDgene. The prioritization analysis resulted in 16 prioritized candidate genes, which are mainly involved in several major neurotransmitter systems or in nervous system development pathways. Among these genes, nervous system development related genes, especially SNAP25, STX1A and the gene-gene interactions related with each of them deserve further investigations. Our results may provide new insight for further verification study and facilitate the exploration of pathogenesis mechanism of ADHD.

Citing Articles

Maternal Immune Activation Induces Neuroinflammation and Cortical Synaptic Deficits in the Adolescent Rat Offspring.

Cieslik M, Gassowska-Dobrowolska M, Jesko H, Czapski G, Wilkaniec A, Zawadzka A Int J Mol Sci. 2020; 21(11).

PMID: 32521803 PMC: 7312084. DOI: 10.3390/ijms21114097.

Integrative data mining highlights candidate genes for monogenic myopathies.

Neto O, Tassy O, Biancalana V, Zanoteli E, Pourquie O, Laporte J PLoS One. 2014; 9(10):e110888.

PMID: 25353622 PMC: 4213015. DOI: 10.1371/journal.pone.0110888.

Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update.

Pavlidis P, Gillis J F1000Res. 2014; 2:230.

PMID: 24715959 PMC: 3962002. DOI: 10.12688/f1000research.2-230.v1.

References

Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F . Gene prioritization through genomic data fusion. Nat Biotechnol. 2006; 24(5):537-44. DOI: 10.1038/nbt1203. View

Lasky-Su J, Neale B, Franke B, Anney R, Zhou K, Maller J . Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. Am J Med Genet B Neuropsychiatr Genet. 2008; 147B(8):1345-54. DOI: 10.1002/ajmg.b.30867. View

Keshava Prasad T, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S . Human Protein Reference Database--2009 update. Nucleic Acids Res. 2008; 37(Database issue):D767-72. PMC: 2686490. DOI: 10.1093/nar/gkn892. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Gizer I, Ficks C, Waldman I . Candidate gene studies of ADHD: a meta-analytic review. Hum Genet. 2009; 126(1):51-90. DOI: 10.1007/s00439-009-0694-x. View

Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, Moreau Y . TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res. 2005; 33(Web Server issue):W393-6. PMC: 1160115. DOI: 10.1093/nar/gki354. View

Flicek P, Amode M, Barrell D, Beal K, Brent S, Chen Y . Ensembl 2011. Nucleic Acids Res. 2010; 39(Database issue):D800-6. PMC: 3013672. DOI: 10.1093/nar/gkq1064. View

Chen J, Aronow B, Jegga A . Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics. 2009; 10:73. PMC: 2657789. DOI: 10.1186/1471-2105-10-73. View

Chen Y, Wang W, Zhou Y, Shields R, Chanda S, Elston R . In silico gene prioritization by integrating multiple data sources. PLoS One. 2011; 6(6):e21137. PMC: 3123338. DOI: 10.1371/journal.pone.0021137. View

10.

Tranchevent L, Capdevila F, Nitsch D, De Moor B, De Causmaecker P, Moreau Y . A guide to web tools to prioritize candidate genes. Brief Bioinform. 2011; 12(1):22-32. DOI: 10.1093/bib/bbq007. View

11.

Faraone S, Perlis R, Doyle A, Smoller J, Goralnick J, Holmgren M . Molecular genetics of attention-deficit/hyperactivity disorder. Biol Psychiatry. 2005; 57(11):1313-23. DOI: 10.1016/j.biopsych.2004.11.024. View

12.

Smoot M, Ono K, Ruscheinski J, Wang P, Ideker T . Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2010; 27(3):431-2. PMC: 3031041. DOI: 10.1093/bioinformatics/btq675. View

13.

Liu S, Sharon-Friling R, Ivanova P, Milne S, Myers D, Rabinowitz J . Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress. Proc Natl Acad Sci U S A. 2011; 108(31):12869-74. PMC: 3150939. DOI: 10.1073/pnas.1109796108. View

14.

Guan L, Wang B, Chen Y, Yang L, Li J, Qian Q . A high-density single-nucleotide polymorphism screen of 23 candidate genes in attention deficit hyperactivity disorder: suggesting multiple susceptibility genes among Chinese Han population. Mol Psychiatry. 2008; 14(5):546-54. DOI: 10.1038/sj.mp.4002139. View

15.

McKusick V . Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet. 2007; 80(4):588-604. PMC: 1852721. DOI: 10.1086/514346. View

16.

Arnsten A . Fundamentals of attention-deficit/hyperactivity disorder: circuits and pathways. J Clin Psychiatry. 2006; 67 Suppl 8:7-12. View

17.

Zhang L, Chang S, Li Z, Zhang K, Du Y, Ott J . ADHDgene: a genetic database for attention deficit hyperactivity disorder. Nucleic Acids Res. 2011; 40(Database issue):D1003-9. PMC: 3245028. DOI: 10.1093/nar/gkr992. View

18.

Neale B, Medland S, Ripke S, Asherson P, Franke B, Lesch K . Meta-analysis of genome-wide association studies of attention-deficit/hyperactivity disorder. J Am Acad Child Adolesc Psychiatry. 2010; 49(9):884-97. PMC: 2928252. DOI: 10.1016/j.jaac.2010.06.008. View

19.

Kang H, Kawasawa Y, Cheng F, Zhu Y, Xu X, Li M . Spatio-temporal transcriptome of the human brain. Nature. 2011; 478(7370):483-9. PMC: 3566780. DOI: 10.1038/nature10523. View

20.

Mulder N, Apweiler R . The InterPro database and tools for protein domain analysis. Curr Protoc Bioinformatics. 2008; Chapter 2:Unit 2.7. DOI: 10.1002/0471250953.bi0207s21. View