Phevor statistics

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Associated diseases

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Phevor specifications

Information


Unique identifier OMICS_04802
Name Phevor
Alternative name PHEnotype driven Variant Ontological Re-ranking tool
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mark Yandell <>

Publication for PHEnotype driven Variant Ontological Re-ranking tool

Phevor in pipelines

 (3)
2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] the “exomiser gene combined score” generated very low values. so, variants with a threshold ≥1.46 × 10−5 were considered as candidate variants. exomiser v2 allows the use of several hpo terms, but phevor only allows five hpo terms. to compare both systems, only five hpo terms were selected for the benchmarking analyses. the five hpo terms most commonly associated with each disease […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] the “exomiser gene combined score” generated very low values. so, variants with a threshold ≥1.46 × 10−5 were considered as candidate variants. exomiser v2 allows the use of several hpo terms, but phevor only allows five hpo terms. to compare both systems, only five hpo terms were selected for the benchmarking analyses. the five hpo terms most commonly associated with each disease […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] to top 10, 20, or 50. roc curves were generated to determine the ability to predict real causal variants based on models consisting of the combination of the five systems (pavar, exomiser v2, vaast-phevor, cadd, and fathmm) and each individual system. in all the cases, the analyses were performed for the top 10, 20, and 50 ranked variants and using different control datasets to filter […]


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Phevor in publications

 (8)
PMCID: 5647373
PMID: 29044180
DOI: 10.1038/s41598-017-13841-y

[…] genes using a random-walk-with-restart algorithm searching gene interaction networks. a bayesian approach is used to evaluate deleterious variants in the exome to known disease-gene associations., phevor integrates phenotype, gene function, and disease information with genomic data targeting both known variation and disease causing alleles not previously implicated in disease. phevor combines […]

PMCID: 5558185
PMID: 28812537
DOI: 10.1186/s12864-017-3910-4

[…] the similarity between the phenotypic profile and disease, and this score is in turn used to rank variants that reside in disease-implicated genes., a number of tools, such as phenolyzer [], phevor2 [], phen-gen [], genecards [], and exomiser [] leverage databases of gene-disease-phenotype relationships and phenotype information to prioritize candidate genes. all of these tools, […]

PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] of heterozygous variants using exome-sequencing datasets in familial meniere disease: an in-house pathogenic variant (pavar) score, the variant annotation analysis and search tool (vaast-phevor), exomiser-v2, cadd, and fathmm. we also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets., pavar and vaast were able to select […]

PMCID: 5650244
PMID: 29367954
DOI: 10.1210/js.2016-1014

[…] mutation taster (http://www.mutationtaster.org/), polyphen (http://genetics.bwh.harvard.edu/pph2), and phylop []. in both analyses, the phenotype driven variant ontological re-ranking tool (phevor) feature was used to further prioritize genes for analysis using premature ovarian failure and poi as filters []., rna was isolated from whole blood from the proband and two women with poi […]

PMCID: 4736244
PMID: 26838676
DOI: 10.1186/s13073-016-0261-8

[…] do so [, ]. alternatively, extasy ranks variants by combining input phenotype similarity scores with scores computed between input genotype data and “fused” human and non-human genomic data, whereas phevor combines input phenotype data with data from human and non-human ontologies to reprioritize externally pre-computed ranks [, ]. as with phen-gen, the inclusion in these analyses […]


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Phevor institution(s)
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA; Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA; Department of Pathology, University of Utah, Salt Lake City, UT, USA; ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA; Omicia Inc., Oakland, CA, USA; Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
Phevor funding source(s)
Supported by the National Institute of General Medical Sciences (NIGMS) grant R01GM104390, NIGMS grant R01GM104390, National Human Genome Research Institute (NHGRI) grant R44HG006579, NHGRI grant R01HG004341, NIH National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) grant R01DK084198, NIDDK grant DK091374 and by grant 1ULTR001067 from the NIH National Center for Advancing Translational Sciences.

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