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NCBI Resources: PheGenI

Contains information about the NCBI databases to be used as a teaching tool.

Phenotype-Genotype Integrator (PheGenI), combines genome-wide association study (GWAS) data with genetic, phenotype, expression, and polymorphism data from the NCBI databases. Users can search based on chromosomal location, gene, SNP, or phenotype. Human records in the Gene database include links to PheGenI when available. PheGenI provides annotated SNPs and gene expression data and also includes a dynamic genomic sequence viewer.

Video Tutorial

Searching PheGenI

You can search PheGenI by Phenotype or Genotype 

Phenotype Selection: users can search for phenotypes using the MeSH vocabulary.

  • Typing phenotypes into the search box will trigger autocompletion
  • You can also browse terms using the browse button
  • If you type in multiple terms, results that include any of them will be included in the results.

 

 

Genotype selection: search based on genetic features

  • Location: select chromosome from the dropdown, type in base pair range
  • Gene: enter gene name or ID
  • SNP: use rs number
  • Can filter on SNP functional class

Search Results

No matter how you search, the results all contain the same sections. 

For example, if you search for the phenotype/trait "hypertension", you will get results in all categories relevant to this phenotype. If you search for a gene name, you'll only get one result in gene, but will pull up studies that had a significant result with the gene. Same with SNP identifiers

Click on the link for the individual records of interest in these categories to get more information.