Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology

Panwen Wang, Wing Fu Lai, Mulin Jun Li, Feng Xu, Hari Krishna Yalamanchili, Robin Lovell-Badge, Junwen Wang

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth.

Original languageEnglish (US)
Article numbere77478
JournalPLoS One
Volume8
Issue number10
DOIs
StatePublished - Oct 23 2013
Externally publishedYes

Fingerprint

protein-protein interactions
Genes
Phenotype
phenotype
Proteins
genes
Genome
Servers
Encyclopedias
Gene Ontology
Genetic Association Studies
Zebrafish
Diptera
Type 2 Diabetes Mellitus
Area Under Curve
genome
Yeasts
methodology
Danio rerio
human diseases

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Wang, P., Lai, W. F., Li, M. J., Xu, F., Yalamanchili, H. K., Lovell-Badge, R., & Wang, J. (2013). Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology. PLoS One, 8(10), [e77478]. https://doi.org/10.1371/journal.pone.0077478

Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology. / Wang, Panwen; Lai, Wing Fu; Li, Mulin Jun; Xu, Feng; Yalamanchili, Hari Krishna; Lovell-Badge, Robin; Wang, Junwen.

In: PLoS One, Vol. 8, No. 10, e77478, 23.10.2013.

Research output: Contribution to journalArticle

Wang, P, Lai, WF, Li, MJ, Xu, F, Yalamanchili, HK, Lovell-Badge, R & Wang, J 2013, 'Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology', PLoS One, vol. 8, no. 10, e77478. https://doi.org/10.1371/journal.pone.0077478
Wang P, Lai WF, Li MJ, Xu F, Yalamanchili HK, Lovell-Badge R et al. Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology. PLoS One. 2013 Oct 23;8(10). e77478. https://doi.org/10.1371/journal.pone.0077478
Wang, Panwen ; Lai, Wing Fu ; Li, Mulin Jun ; Xu, Feng ; Yalamanchili, Hari Krishna ; Lovell-Badge, Robin ; Wang, Junwen. / Inference of Gene-Phenotype Associations via Protein-Protein Interaction and Orthology. In: PLoS One. 2013 ; Vol. 8, No. 10.
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