Phen-Gen statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

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 Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

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 Yes

Taxon


  • Primates
    • Homo sapiens

Publication for Phen-Gen

Phen-Gen citations

 (9)
library_books

Evaluating phenotype driven approaches for genetic diagnoses from exomes in a clinical setting

2017
Sci Rep
PMCID: 5647373
PMID: 29044180
DOI: 10.1038/s41598-017-13841-y

[…] of matching. However, as we have shown here for cases in a clinical setting, tools which have a gene discovery rather than diagnostic emphasis may give misleading results.Most tools (eXtasy, Phevor, Phen-Gen, OVA and Exomiser hiPHIVE) integrate human and non-human genomic data which underlies their gene discovery focus. Our analyses, which utilise clinical exome data with known molecular causes, […]

library_books

Leveraging network analytics to infer patient syndrome and identify causal genes in rare disease cases

2017
BMC Genomics
PMCID: 5558185
PMID: 28812537
DOI: 10.1186/s12864-017-3910-4

[…] Some tools leverage integration with other tools to provide this capability (Phevor2 + VAAST [], Phenolyzer + ANNOVAR [], PDR + Ingenuity Variant Analysis), while others offer it as part of the tool (Phen-Gen, Exomiser). Similarly, by partnering or independently, many of these tools (Phevor2 + VAAST, PDR + Ingenuity Variant Analysis, Phen-Gen, Exomiser) can provide family-based analysis involving […]

library_books

The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype

2017
Int J Mol Sci
PMCID: 5344004
PMID: 28241430
DOI: 10.3390/ijms18020472

[…] te 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 of sin […]

library_books

iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes

2016
Genome Med
PMCID: 5180414
PMID: 28007024
DOI: 10.1186/s13073-016-0390-0

[…] ation prioritization fail to exceed 81% accuracy in detecting real cancer driver mutations. Mutation prioritization tools for personal cancer genomes, on the other hand, are extremely underdeveloped. Phen-Gen is one of the few tools for prioritizing personal disease driver genes using only mutations identified from next-generation sequencing []. Similarly, wANNOVAR/Phenolyzer is a combination of t […]

library_books

The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges

2016
PMCID: 4959014
PMID: 27504451
DOI: 10.3389/fcvm.2016.00022

[…] hms using multiple features, such as the predicted effect of a variant on protein function (). Variant prioritization applications that incorporate human phenotype data in this manner include Phevor, Phen-Gen, and Exomiser (–). There is evidence that incorporation of structured human phenotype data does improve performance (). Importantly, computational algorithms based on semantic similarity to c […]

library_books

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome wide diagnostics

2016
Genome Med
PMCID: 4736244
PMID: 26838676
DOI: 10.1186/s13073-016-0261-8

[…] d Resnik similarity approaches assigned to the reported variants median ranks in the top 1 % of all filtered variants (Fig. ).Fig. 3We compared the performance of the OE transitive maximum to that of Phen-Gen [], eXtasy [], PhenIX [], PHIVE [], and hiPHIVE []. Because the latter three were implemented via Exomiser, which allows for variant filtration by MAF, we applied a filter of 1 % MAF. Because […]

Citations

Looking to check out a full list of citations?

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

Phen-Gen reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Phen-Gen