Endometriosis Knowledgebase

A database for endometriosis-associated genes

Key Points

Highlight:

• This article introduces an open endometriosis knowledgebase, which is a database containing information on endometriosis-related genes that is available to the public.

Importance:

• The database is a great resource for the researcher and anyone wishing to learn more about endometriosis-related genes.

What's done here:

• Endometriosis is a polygenic condition and affects different ethnic populations. Current literature and information about genetic factors of endometriosis are scattered, making it hard to define meaningful gene networks to improve endometriosis diagnosis and treatment.
• The aim of this study was to develop a resource that contains all genes associated with endometriosis. Such knowledgebase is a manually curated information on endometriosis genes and holds information on 831 genes, together with their polymorphisms, gene ontology, pathways, and diseases.

Data:

• Endometriosis associated genes in the database are enriched in cell signaling, immune regulation, and reproduction pathways.
• Endometriosis shows overlapping genes with cancers, endocrine/reproductive, nervous system, immune and metabolic diseases.
• The endometriosis knowledgebase may benefit researchers and clinicians working to better understand endometriosis.

Limitation:

• While the study provides a comprehensive database, it lacks information regarding endometriosis stages and/or severity.

Lay Summary

Several studies have pointed to possible genetic factors in endometriosis. Targeted gene-based and high-throughput methods such as Genome-Wide Association Studies (GWAS) have been previously employed to identify endometriosis-associated genes.

However, the accuracy of these data are difficult to evaluate and can vary when studies in other larger cohorts. Therefore, endometriosis is genetically complex and require a more integrated method to provide meaningful study outcome.

The current study by Joseph et al. from the National Institute for Research in Reproductive Health, Mumbai, India build a manually curated knowledge base that serves as a resource which contains all the genes associated with endometriosis. It is hoped that this knowledge base would be a comprehensive tool that can help to improve endometriosis research.

To generate the database, the authors queried PubMed database and genes/single nucleotide polymorphisms (SNPs) information from the National Center for Biotechnology Information (NCBI). In total, the knowledge base consists of information on 831 genes and their 302 SNPs, 7032 gene ontologies, 367 pathways, and 1390 diseases. This database is available through the link http://www.ek.bicnirrh.res.in/ and allows users to search and browse endometriosis-associated genes. Information on the gene mutation, population size, ethnicity, and other pathology are included in the database. Moreover, the database also shows information regarding gene ontology, pathways, and other associated disorders. These features allow gene-disease networks analyses and help to delineate the complex genetic factors related to endometriosis.

The analysis showed that endometriosis-related genes were enriched in cell-signaling molecules and transcription factors, at the same time steroid hormone receptor, inflammation and angiogenesis pathways. Endometriosis also shares overlapping genes with cancers, diseases related to the endocrine/reproductive, nervous system, immune and metabolic. Hence, this knowledge base may help to improve understanding of the genetic landscape of endometriosis.

Research Source: https://www.ncbi.nlm.nih.gov/pubmed/31169291