Cited by 194Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental DisordersGenetic Associations and Epidemiology

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AutismKB: an evidence-based knowledgebase of autism genetics

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Xu, Li-Ming, Li, Jia-Rui, Huang, Yue, Zhao, Min, Tang, Xing, Wei, Liping·2012·Nucleic Acids Research

DOI 10.1093/nar/gkr1145PMC PMC3245106

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Abstract

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.

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Additional file 5 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
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Additional file 1 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
Liu, H., Barnes, J., Pedrosa, E., Herman, N. S., Salas, F., Wang, P., Zheng, D., & Lachman, H. M. (2020) · Figshare · doi:10.6084/m9.figshare.12285389
Additional file 7 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
Liu, H., Barnes, J., Pedrosa, E., Herman, N. S., Salas, F., Wang, P., Zheng, D., & Lachman, H. M. (2020) · Figshare · doi:10.6084/m9.figshare.12285440
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Martínez-Minguet, D., Noël, R., Alberto García, S., Costa, M., & Pastor, O. (2025) · Database · doi:10.1093/database/baaf067 · Cited by 1
Additional file 3 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
Liu, H., Barnes, J., Pedrosa, E., Herman, N. S., Salas, F., Wang, P., Zheng, D., & Lachman, H. M. (2020) · Figshare · doi:10.6084/m9.figshare.12285410
Additional file 2 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
Liu, H., Barnes, J., Pedrosa, E., Herman, N. S., Salas, F., Wang, P., Zheng, D., & Lachman, H. M. (2020) · Figshare · doi:10.6084/m9.figshare.12285398
Additional file 11 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704650
Self-citation
Additional file 8 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704641
Self-citation
Additional file 6 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704635
Self-citation
Additional file 10 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704647
Self-citation
Additional file 9 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704644
Self-citation
Additional file 4 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
Liu, H., Barnes, J., Pedrosa, E., Herman, N. S., Salas, F., Wang, P., Zheng, D., & Lachman, H. M. (2020) · Figshare · doi:10.6084/m9.figshare.12285416
Additional file 3 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704626
Self-citation
Additional file 4 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704629
Self-citation
Additional file 2 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704623
Self-citation
Additional file 7 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704638
Self-citation
Additional file 6 of Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations
Liu, H., Barnes, J., Pedrosa, E., Herman, N. S., Salas, F., Wang, P., Zheng, D., & Lachman, H. M. (2020) · Figshare · doi:10.6084/m9.figshare.12285431
Additional file 5 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704632
Self-citation
Additional file 1 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704620
Self-citation
Additional file 12 of Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)
Tan, Y., Huang, Y., Xu, C., Huang, X., Li, S., & Yin, Z. (2024) · Figshare · doi:10.6084/m9.figshare.26704653
Self-citation
BRD1 haploinsufficiency alters early neuronal programming and disrupts maturation in human induced glutamatergic neuronsPreprint
Donskov, J. G., Deans, P. M., Pediotidis-Maniatis, D., Høgfeldt, J. E., Børglum, A. D., Denham, M., Brennand, K., & Qvist, P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.19.695380
Cerebellar microglia-derived IL-17A mitigates autism-related behavioral and synaptic deficits
Yin, J., Li, W., Shen, L.-P., Zhang, W.-L., Chen, J.-Y., Zhang, B.-B., Chen, Y., Li, T., Li, H., Gao, Z., et al. (2026) · Molecular Psychiatry · doi:10.1038/s41380-026-03454-1 · Cited by 1
BRD1 haploinsufficiency alters early neuronal programming and disrupts maturation in human induced glutamatergic neuronsPreprint
Qvist, P., Donskov, J. G., Deans, M., Pediotidis-Maniatis, D., Høgfeldt, J. E., Børglum, A. D., Denham, M., & Brennand, K. (2026) · Research Square · doi:10.21203/rs.3.rs-8417267/v1
Identification of Peripheral Blood mIR-128-3p Molecular Signature in Children with Autism Spectrum Disorder
Popov, T., Minchev, S., & Vachev, T. I. (2026) · Balkan Journal of Medical Genetics · doi:10.2478/bjmg-2026-0009

Authors: Xu, L.-M., Li, J.-R., Huang, Y., Zhao, M., Tang, X., & Wei, L.
Affiliations: Peking University (CN)
Corresponding author: Wei, Liping
ORCID: Zhao, Min
Tang, Xing
Wei, Liping
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2011-12-01
Volume: 40
Issue: D1
Pages: D1016-D1022
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkr1145
PMC: PMC3245106
OpenAlex: W2039778388
Cited by: 179
References: 65
Citations by year: 2026: 4 · 2025: 9 · 2024: 5 · 2023: 6 · 2022: 9 · 2021: 6 · 2020: 14 · 2019: 8 · 2018: 19 · 2017: 14 · 2016: 16 · 2015: 14 · 2014: 21 · 2013: 22 · 2012: 12
FWCI: 8.94
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/3.0 (vor, 1989 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Natural Science Foundation of China (31025014, 2011CBA01102)
Topics: Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords: autism spectrum disorder, autism genetics, gene ranking, copy number variation, single nucleotide polymorphisms, linkage region, neurodevelopmental disorders, axon guidance, neuroactive ligand-receptor interaction, gene expression profiling, protein-protein interaction, animal models, pharmacogenetics
MeSH terms: Autistic Disorder, Humans, Genetic Linkage, User-Computer Interface, Genetic Variation, Databases, Genetic, Knowledge Bases, Molecular Sequence Annotation

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