Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans

Zhao, Guizhe; Li, Kuokuo; Li, Bin; Wang, Zheng; Fang, Zhenghuan; Wang, Xiaomeng; Zhang, Yi; Luo, Tengfei; Zhou, Qiao; Wang, Lin; Xie, Yi; Wang, Yijing; Chen, Qian; Lu, Xia; Tang, Yu; Tang, Beisha; Xia, Kun; Li, Jinchen

doi:10.1093/nar/gkz923

Cited by 45 publications

(68 citation statements)

References 144 publications

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“…NDex is the latest in a number of community resources that have integrated DGIdb. Existing data clients include GeneCards ( 8 ), BioGPS ( 9 ), CancerTracer ( 10 ), Gene4Denovo ( 11 ), SL-BioDP ( 12 ), TargetDB ( 13 ) and OncoGemini ( 14 ), among others.…”

Section: Introductionmentioning

confidence: 99%

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

Freshour

Kiwala

Cotto

et al. 2020

Nucleic Acids Research

654

435

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The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normalized and merged into conceptual groups. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major version release of this database. A primary focus of this update was integration with crowdsourced efforts, leveraging the Drug Target Commons for community-contributed interaction data, Wikidata to facilitate term normalization, and export to NDEx for drug-gene interaction network representations. Seven new sources have been added since the last major version release, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include the introduction of a more sophisticated Query Score for interaction search results, an updated Interaction Score, the inclusion of interaction directionality, and several additional improvements to search features, data releases, licensing documentation and the application framework.

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Section: Introductionmentioning

confidence: 99%

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

Freshour

Kiwala

Cotto

et al. 2020

Nucleic Acids Research

654

435

View full text Add to dashboard Cite

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“…Targeted sequencing [24][25][26][27] , whole-exome sequencing (WES) [28][29][30][31][32][33][34] , and whole-genome sequencing (WGS) 35,36 have been successfully used by our group and others in detecting de novo mutations (DNMs) to prioritize risk genes for ASD. These coding DNMs have been estimated to contribute to 20-40% of ASD diagnoses 33,37,38 . In addition, integrated protein-protein interaction (PPI) and co-expression networks for ASD risk genes with functional DNMs indicate that risk genes are associated with biological processes related to Wnt signaling, chromatin remodeling, transcriptional regulation, and synaptic functions [39][40][41][42][43][44] .…”

Section: Introductionmentioning

confidence: 99%

Genetic evidence of gender difference in autism spectrum disorder supports the female-protective effect

Zhang

et al. 2020

Transl Psychiatry

Self Cite

117

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Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with a male-to-female prevalence of 4:1. However, the genetic mechanisms underlying this gender difference remain unclear. Mutation burden analysis, a TADA model, and co-expression and functional network analyses were performed on de novo mutations (DNMs) and corresponding candidate genes. We found that the prevalence of putative functional DNMs (loss-of-function and predicted deleterious missense mutations) in females was significantly higher than that in males, suggesting that a higher genetic load was required in females to reach the threshold for a diagnosis. We then prioritized 174 candidate genes, including 60 shared genes, 91 male-specific genes, and 23 female-specific genes. All of the three subclasses of candidate genes were significantly more frequently co-expressed in female brains than male brains, suggesting that compensation effects of the deficiency of ASD candidate genes may be more likely in females. Nevertheless, the three subclasses of candidate genes were co-expressed with each other, suggesting a convergent functional network of male and female-specific genes. Our analysis of different aspects of genetic components provides suggestive evidence supporting the female-protective effect in ASD. Moreover, further study is needed to integrate neuronal and hormonal data to elucidate the underlying gender difference in ASD.

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“…Previously, DGIdb has been integrated with other community resources such as GeneCards (24), which uses DGIdb as a source for interactions between GeneCards gene entries and drugs, and BioGPS (25), which offers a DGIdb plug-in for searching drug-gene interactions. Since the publication of DGIdb 3.0, DGIdb has been regularly integrated with additional resources such as CancerTracer (26), Gene4Denovo (27), SL-BioDP(28), TargetDB (29), and OncoGemini (30).…”

Section: Integration With Ndex and Other External Resourcesmentioning

confidence: 99%

Integration of the Drug-Gene Interaction Database (DGIdb) with open crowdsource efforts

Freshour

Kiwala

Cotto

et al. 2020

Preprint

View full text Add to dashboard Cite

The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from various sources including publications, databases, and other web-based sources in one resource. These drug, gene, and interaction claims are normalized and grouped to identify aliases, merge concepts, and reduce redundancy. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major update of this database. Seven new sources have been added, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include further development of automatic jobs for routine data updates, more sophisticated query scores for interaction search results, extensive manual curation of interaction source link outs, and the inclusion of interaction directionality. A major focus of this update was integration with crowd-sourced efforts, including leveraging the curation activities of Drug Target Commons, using Wikidata to facilitate term normalization, and integrating into NDEx for producing network representations.

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Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans

Cited by 45 publications

References 144 publications

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

Genetic evidence of gender difference in autism spectrum disorder supports the female-protective effect

Integration of the Drug-Gene Interaction Database (DGIdb) with open crowdsource efforts

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