AutismKB: An evidence-based knowledgebase of autism genetics

L M Xu; Jia-Rui Li; Y Huang; Min Zhao; X Tang; L Wei

doi:10.1093/nar/gkr1145

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AutismKB: An evidence-based knowledgebase of autism genetics

Journal article

Open access

Peer reviewed

AutismKB: An evidence-based knowledgebase of autism genetics

L M Xu, Jia-Rui Li, Y Huang, Min Zhao, X Tang and L Wei

Nucleic Acids Research, Vol.40(D1), pp.D1016-D1022

2012

DOI: https://doi.org/10.1093/nar/gkr1145

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Abstract

autism

AutismKB data base

copy number variation

gene expression profiling

gene mapping

genetic association

genetic linkage

human

knowledge base

prevalence

protein protein interaction

scoring system

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a prevalence of 0.9-2.6%. Twin studies showed a heritability of 38-90%, indicating strong genetic contributions. Yet it is unclear how many genes have been associated with ASD and how strong the evidence is. A comprehensive review and analysis of literature and data may bring a clearer big picture of autism genetics. We show that as many as 2193 genes, 2806 SNPs/VNTRs, 4544 copy number variations (CNVs) and 158 linkage regions have been associated with ASD by GWAS, genome-wide CNV studies, linkage analyses, low-scale genetic association studies, expression profiling and other low-scale experimental studies. To evaluate the evidence, we collected metadata about each study including clinical and demographic features, experimental design and statistical significance, and used a scoring and ranking approach to select a core data set of 434 high-confidence genes. The genes mapped to pathways including neuroactive ligand-receptor interaction, synapse transmission and axon guidance. To better understand the genes we parsed over 30 databases to retrieve extensive data about expression patterns, protein interactions, animal models and pharmacogenetics. We constructed a MySQL-based online database and share it with the broader autism research community at http://autismkb.cbi.pku. edu.cn, supporting sophisticated browsing and searching functionalities. © The Author(s) 2011. Published by Oxford University Press.

Details

Title: AutismKB: An evidence-based knowledgebase of autism genetics
Authors: L M Xu (Author) - Peking University, China
Jia-Rui Li (Author) - Peking University, China
Y Huang (Author) - Peking University, China
Min Zhao (Author) - Peking University, China
X Tang (Author) - Peking University, China
L Wei (Author) - Peking University, China
Publication details: Nucleic Acids Research, Vol.40(D1), pp.D1016-D1022
Publisher: Oxford University Press
Date published: 2012
DOI: 10.1093/nar/gkr1145
ISSN: 0305-1048
Copyright note: Copyright © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99448859402621
Output Type: Journal article

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