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PhenPath: a tool for characterizing biological functions underlying different phenotypes.

Giulia Babbi1,2, Pier Luigi Martelli3,4, Rita Casadio1,5,6

  • 1University of Bologna, FABIT, Via San Donato 15, 40126, Bologna, Italy.

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|July 17, 2019
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Summary
This summary is machine-generated.

PhenPathDB and PhenPathTOOL offer a novel resource for understanding disease mechanisms by linking phenotypes to genes and biological functions. This aids researchers in investigating complex diseases with multiple symptoms.

Keywords:
Biological processDiseasesEnrichmentMolecular pathwayPhenotype

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Area of Science:

  • Genomics
  • Systems Biology
  • Bioinformatics

Background:

  • Diseases often present with complex symptom patterns, necessitating tools to link phenotypes to molecular functions.
  • Understanding gene-disease-phenotype relationships is crucial for formulating hypotheses about disease origins.

Purpose of the Study:

  • To introduce PhenPath, a resource comprising a database (PhenPathDB) and a tool (PhenPathTOOL).
  • To facilitate the investigation of molecular causes underlying diseases with multiple phenotypic manifestations.

Main Methods:

  • PhenPathDB integrates human genes with phenotypes from Human Phenotype Ontology (HPO) and OMIM Clinical Synopses.
  • A network-based method (NET-GE) associates phenotypes with biological functions and pathways.
  • PhenPathTOOL analyzes user-defined phenotype sets to identify shared diseases, genes, and functional terms.

Main Results:

  • PhenPathDB contains data for 7137 HPO phenotypes, 4292 diseases, and 3446 genes.
  • A significant percentage of HPO phenotypes are enriched for Gene Ontology terms (87.7% Biological Process, 86.9% Molecular Function, 73.6% Cellular Component).
  • Enrichment for KEGG (58.8%) and Reactome (77.8%) pathways was observed for HPO phenotypes.

Conclusions:

  • PhenPath provides valuable molecular insights for studying diseases with multiple phenotypes.
  • The resource aids researchers and physicians in identifying molecular mechanisms and functions associated with co-occurring phenotypes.
  • PhenPath is freely accessible online.