GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes

Abstract

Mammalian gestation and pregnancy are fast evolving processes that involve the interaction of the fetal, maternal and paternal genomes. Version 1.0 of the GEneSTATION database (http://genestation.org) integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. GEneSTATION is built using tools from the Generic Model Organism Database project, including the biology-aware database CHADO, new tools for rapid data integration, and algorithms that streamline synthesis and user access. GEneSTATION contains curated life history information on pregnancy and reproduction from 23 high-quality mammalian genomes. For every human gene, GEneSTATION contains diverse evolutionary (e.g. gene age, population genetic and molecular evolutionary statistics), organismal (e.g. tissue-specific gene and protein expression, differential gene expression, disease phenotype), and molecular data types (e.g. Gene Ontology Annotation, protein interactions), as well as links to many general (e.g. Entrez, PubMed) and pregnancy disease-specific (e.g. PTBgene, dbPTB) databases. By facilitating the synthesis of diverse functional and evolutionary data in pregnancy-associated tissues and phenotypes and enabling their quick, intuitive, accurate and customized meta-analysis, GEneSTATION provides a novel platform for comprehensive investigation of the function and evolution of mammalian pregnancy.

Enabling precision medicine in neonatology, an integrated repository for preterm birth research

“…However, the database is limited to disease-gene and pathway associations. GEneSTATION 23 is a comprehensive database that integrates cross-species genomic, transcriptomic, and evolutionary data to advance the understanding of the genetic basis of gestation - and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. This resource specifically focuses on evolutionary and genomic data and is not designed for capturing other ‘omics’ technologies that cannot be directly mapped to human genes or genetic elements (e.g., microbiome data).…”

Genome-wide maps of distal gene regulatory enhancers active in the human placenta

“…More accurate interpretation of these and future GWAS hits is necessary for understanding the complex biology of pregnancy and eventually improving the identification and prevention of disorders such as preterm birth. To facilitate the use of our enhancer maps, they are now integrated into the GEneSTATION web platform for studying pregnancy and preterm birth [19].…”

“…These predicted enhancers provide candidate regions for researchers to test in vitro , and propose mechanisms of action for variants found through GWAS. To facilitate their use, all the enhancer predictions are integrated into GEneSTATION (v2.0) [19].…”