PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants.

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Embargo End Date

ICR Authors

Houlston, Richard

Authors

Ofoegbu, TC
David, A
Kelley, LA
Mezulis, S
Islam, SA
Mersmann, SF
Strömich, L
Vakser, IA
Houlston, RS
Sternberg, MJE

Document Type

Journal Article

Date

2019-06-14

Date Accepted

2019-04-29

Abstract

PhyreRisk is an open-access, publicly accessible web application for interactively bridging genomic, proteomic and structural data facilitating the mapping of human variants onto protein structures. A major advance over other tools for sequence-structure variant mapping is that PhyreRisk provides information on 20,214 human canonical proteins and an additional 22,271 alternative protein sequences (isoforms). Specifically, PhyreRisk provides structural coverage (partial or complete) for 70% (14,035 of 20,214 canonical proteins) of the human proteome, by storing 18,874 experimental structures and 84,818 pre-built models of canonical proteins and their isoforms generated using our in house Phyre2. PhyreRisk reports 55,732 experimentally, multi-validated protein interactions from IntAct and 24,260 experimental structures of protein complexes. Another major feature of PhyreRisk is that, rather than presenting a limited set of precomputed variant-structure mapping of known genetic variants, it allows the user to explore novel variants using, as input, genomic coordinates formats (Ensembl, VCF, reference SNP ID and HGVS notations) and Human Build GRCh37 and GRCh38. PhyreRisk also supports mapping variants using amino acid coordinates and searching for genes or proteins of interest. PhyreRisk is designed to empower researchers to translate genetic data into protein structural information, thereby providing a more comprehensive appreciation of the functional impact of variants. PhyreRisk is freely available at http://phyrerisk.bc.ic.ac.uk.

Citation

Journal of molecular biology, 2019, 431 (13), pp. 2460 - 2466

DOI

10.1016/j.jmb.2019.04.043

URI

https://repository.icr.ac.uk/handle/internal/3692

Rights

https://creativecommons.org/licenses/by/4.0

Source Title

Publisher

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD

ISSN

0022-2836

eISSN

1089-8638

Collections

Genetics and Epidemiology

Research Team

Cancer Genomics

Notes