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PhenoDigm specifications


Unique identifier OMICS_03289
Name PhenoDigm
Alternative name PHENOtype comparisons for DIsease and Gene Models
Restrictions to use None
Maintained Yes

Publication for PHENOtype comparisons for DIsease and Gene Models

PhenoDigm citations


Genetic Variants in Isolated Ebstein Anomaly Implicated in Myocardial Development Pathways

PLoS One
PMCID: 5082909
PMID: 27788187
DOI: 10.1371/journal.pone.0165174

[…] s sequenced include: three genes previously associated with EA (NKX2-5, GATA4, and MYH7), six sarcomere genes, seven genes from candidate EA-associated CNVs identified in this study, 14 highly ranked PhenoDigm [] genes from regions where one or more EA cases had loss of heterozygosity, nine genes in a critical region for EA identified via linkage study in a canine model [], six cardiomyopathy gene […]


GeneTIER: prioritization of candidate disease genes using tissue specific gene expression profiles

PMCID: 4528628
PMID: 25861967
DOI: 10.1093/bioinformatics/btv196

[…] orporates gene expression data from 79 normal human tissues found in Gene Expression Atlas, comparing gene expression between candidate and user-supplied seed genes across tissues. A recent update to PhenoDigm ( ) has incorporated tissue-specific, binary mouse gene expression data from 21 mouse tissues and derived phenotype-tissue associations in order to supplement its phenotype-based queries.Non […]


Similarity based search of model organism, disease and drug effect phenotypes

J Biomed Semantics
PMCID: 4355138
PMID: 25763178
DOI: 10.1186/s13326-015-0001-9

[…] ble in the OMIM repository, while PhenomeNET 2 uses a larger repository and can search phenotypes across multiple model organism species, diseases and drug effect profiles.Another related software is PhenoDigm [], a system similar to PhenomeNET in that it precomputes similarity between model organisms and diseases. PhenoDigm does not currently support user-defined queries over its repository of ph […]


Using association rule mining to determine promising secondary phenotyping hypotheses

PMCID: 4059059
PMID: 24932005
DOI: 10.1093/bioinformatics/btu260

[…] Among other tools for disease gene candidate prediction, PhenoDigm uses phenotype annotations to predict gene candidates underlying a disease (). Disease gene candidates are predicted based on the primary phenotype annotations assigned to mouse and zebrafis […]


A Novel Null Homozygous Mutation Confirms CACNA2D2 as a Gene Mutated in Epileptic Encephalopathy

PLoS One
PMCID: 3864908
PMID: 24358150
DOI: 10.1371/journal.pone.0082154
call_split See protocol

[…] uency, predicted pathogenicity, inheritance pattern and model organism phenotype data. Scores are based on Mutation Taster , SIFT and Polyphen2 for predicted pathogenicity of mutations and on Mouse PhenoDigm for phenotypical overlap with the animal model. We adopted the following criteria: 1) autosomal recessive model; 2) phenotypic classification according to the HPO (Human Phenotype Ontology) […]


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PhenoDigm institution(s)
Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB, UK

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