The personal genome browser: visualizing functions of genetic variants

Juan, Liran; Teng, Mingxiang; Zang, Tianyi; Hao, Yafeng; Wang, Zhenxing; Yan, Chengwu; Liu, Yongzhuang; Li, Jie; Zhang, Tianjiao; Wang, Yadong

doi:10.1093/nar/gku361

Cited by 8 publications

(3 citation statements)

References 31 publications

(42 reference statements)

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“…Annotation information were either stored in MySQL database or flat files indexed by Tabix ( 41 ). We used Circos ( 42 ) to generate global GWASdb v2 SNPs Manhattan plot and personal genome browser (PGB) ( 43 ) to display important annotation tracks.…”

Section: Methodsmentioning

confidence: 99%

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

et al. 2015

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Genome-wide association studies (GWASs), now as a routine approach to study single-nucleotide polymorphism (SNP)-trait association, have uncovered over ten thousand significant trait/disease associated SNPs (TASs). Here, we updated GWASdb (GWASdb v2, http://jjwanglab.org/gwasdb) which provides comprehensive data curation and knowledge integration for GWAS TASs. These updates include: (i) Up to August 2015, we collected 2479 unique publications from PubMed and other resources; (ii) We further curated moderate SNP-trait associations (P-value < 1.0×10−3) from each original publication, and generated a total of 252 530 unique TASs in all GWASdb v2 collected studies; (iii) We manually mapped 1610 GWAS traits to 501 Human Phenotype Ontology (HPO) terms, 435 Disease Ontology (DO) terms and 228 Disease Ontology Lite (DOLite) terms. For each ontology term, we also predicted the putative causal genes; (iv) We curated the detailed sub-populations and related sample size for each study; (v) Importantly, we performed extensive function annotation for each TAS by incorporating gene-based information, ENCODE ChIP-seq assays, eQTL, population haplotype, functional prediction across multiple biological domains, evolutionary signals and disease-related annotation; (vi) Additionally, we compiled a SNP-drug response association dataset for 650 pharmacogenetic studies involving 257 drugs in this update; (vii) Last, we improved the user interface of website.

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Section: Methodsmentioning

confidence: 99%

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

et al. 2015

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“…Given the growth of the JavaScript/HTML5/SVG visualization platform, graphics-rich biomedical web applications using these technologies have been appearing, such as Regulome Explorer and the Personal Genome Browser 12 . These same technologies have also made it possible for us to now replace the JWS-based BioTapestry Viewer with a new web application.…”

Section: Introductionmentioning

confidence: 99%

BioTapestry now provides a web application and improved drawing and layout tools

2016

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Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of both the network architecture and its dynamic evolution over time and space. Interactive visualization tools better enable researchers to conceptualize, understand, and share GRN models. BioTapestry is an established application designed to fill this role, and recent enhancements released in Versions 6 and 7 have targeted two major facets of the program. First, we introduced significant improvements for network drawing and automatic layout that have now made it much easier for the user to create larger, more organized network drawings. Second, we revised the program architecture so it could continue to support the current Java desktop Editor program, while introducing a new BioTapestry GRN Viewer that runs as a JavaScript web application in a browser. We have deployed a number of GRN models using this new web application. These improvements will ensure that BioTapestry remains viable as a research tool in the face of the continuing evolution of web technologies, and as our understanding of GRN models grows.

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“…23andMe is a service company that provides genetic testing for inherited disorders and ancestry-related analysis [ 14 ]. Other related work includes integration of multiple databases for annotation [ 15 ], visualization or manipulation [ 16 ], and analysis and knowledge discovery [ 15 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Virtual Pharmacist: A Platform for Pharmacogenomics

et al. 2015

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We present Virtual Pharmacist, a web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF) files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity at one glance. Batch submission facilitates multivariate analysis or data mining of targeted groups. Individual analysis consists of a report that is readily comprehensible to patients and practioners who have basic knowledge in pharmacology, a table that summarizes variants and potential affected drug response according to the US Food and Drug Administration pharmacogenomic biomarker labeled drug list and PharmGKB, and visualization of a gene-drug-target network. Group analysis provides the distribution of the variants and potential affected drug response of a target group, a sample-gene variant count table, and a sample-drug count table. Our analysis of genomes from the 1000 Genome Project underlines the potentially differential drug responses among different human populations. Even within the same population, the findings from Watson’s genome highlight the importance of personalized medicine. Virtual Pharmacist can be accessed freely at http://www.sustc-genome.org.cn/vp or installed as a local web server. The codes and documentation are available at the GitHub repository (https://github.com/VirtualPharmacist/vp). Administrators can download the source codes to customize access settings for further development.

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The personal genome browser: visualizing functions of genetic variants

Cited by 8 publications

References 31 publications

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

BioTapestry now provides a web application and improved drawing and layout tools

Virtual Pharmacist: A Platform for Pharmacogenomics

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