Phen-Gen specifications

Information


Unique identifier OMICS_09741
Name Phen-Gen
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability No
Maintained No

Taxon


  • Primates
    • Homo sapiens

Versioning


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Information


Unique identifier OMICS_09741
Name Phen-Gen
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Version 1.0
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

Publication for Phen-Gen

Phen-Gen in publications

 (7)
PMCID: 5647373
PMID: 29044180
DOI: 10.1038/s41598-017-13841-y

[…] target being the prioritisation of known and novel disease genes. gene scores are optimised using a random forest model to classify each candidate gene and obtain final ranks for candidate genes., phen-gen predicts the damaging impact of coding mutations (nonsynonymous, splice site, and indels) enabling a quantitative comparison between them. phen-gen determines potential disease impacts […]

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

[…] 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, including pdr, […]

PMCID: 5344004
PMID: 28241430
DOI: 10.3390/ijms18020472

[…] multiple genetically-correlated traits with desired genetic parameters and underlying genetic architectures. pathway-based methods group mutations from genes in a biologically-relevant pathway []. phen-gen is a method that combines the phenotype and the genotype aiming to analyze rare traits []. the method includes an online software tool to analyze data []. rare traits may be the result […]

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

[…] rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in omim morbidmap genes. our tool outperformed phen-gen, extasy, phenix, phive, and hiphive in the prioritization of these clinically reported variants., our integrative paradigm can improve efficiency and, potentially, the quality of genomic […]

PMCID: 4916229
PMID: 26562225
DOI: 10.1038/gim.2015.137

[…] number of genes that have phenotypic information and the amount of phenotypic data associated with a gene, it still requires that phenotype data are available for the gene containing the variant. phen-gen utilizes phenotype matching and a random-walking algorithm, but without taking advantage of model organism data; its benchmarking, using the same strategy with 1000 genome project exomes, […]


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Phen-Gen institution(s)
Computational and Systems Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore

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