GDDP
GDDP is a web application to demonstrate the methods that we developed to prioritize diagnosis of genetic diseases based on phenotypes. Method 1 is based on integrated semantic similarity and Method 2 is based on ontological overlap test between the phenotypes expressed by a patient and phenotypes annotated to known diseases.
- Chen, Jing, et al. “Novel phenotype–disease matching tool for rare genetic diseases.” Genetics in Medicine 21.2 (2019): 339-346.(link)
GDDPV
GDDPV is a web application to prioritize pathogenic variants based on sequence data (VCF file) and phenotypes (free text) of a patient with genetic disease. Variants detected in a patient are annotated by allele frequencies, genes, and prioritized by phenotypes of the patient based on GDDP Method 2 separately for different inheritance patterns.
The application is under development.
ToppGene
ToppGene is a web application for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. Gene list enrichment detects functional enrichment of a gene list based on Transcriptome, Proteome, Regulome (TFBS and miRNA), Ontologies (GO, Pathway), Phenotype (human disease and mouse phenotype), Pharmacome (Drug-Gene associations), literature co-citation, and other features. Functional annotation-based disease candidate gene prioritization integrates multiple functional annotations using a meta-analysis framework. The protein–protein interaction network (PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method).
- Chen, Jing, et al. “ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.” Nucleic acids research 37.suppl_2 (2009): W305-W311.(link)
- Chen, Jing, Bruce J. Aronow, and Anil G. Jegga. “Disease candidate gene identification and prioritization using protein interaction networks.” BMC bioinformatics 10.1 (2009): 73.(link)
- Chen, Jing, et al. “Improved human disease candidate gene prioritization using mouse phenotype.” BMC bioinformatics 8.1 (2007): 392.(link)