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

Mara Kim,Haley R Eidem,Rohit Venkat,J Anthony Capra,Louis J Muglia,Scott M Williams,Julie B Phillips,Antonis Rokas,Kenneth Petren,Kriston L Mcgary,Sashank Nutakki,Jibril Hirbo,Brian A Cooper,Patrick Abbot

doi:10.1093/nar/gkv1137

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.

Highlights

Placental mammals, which originated 160 million years ago, uniformly share a conserved set of reproductive traits related to embryonic development within a uterus and nutrient provisioning through a chorioallantoic placenta [1]
We have developed GEneSTATION, a database that integrates diverse types of -omics data across mammals to advance understanding of the genetic basis of pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans
Understanding the complex functional landscape of pregnancy, how abnormalities of pregnancy arise, or how the biological mechanisms of gestation evolve and translate between species can be greatly augmented by the integration and synthesis of multiple types of experimental data, genomic data, and evolutionary analyses

Summary

INTRODUCTION

Placental mammals, which originated 160 million years ago, uniformly share a conserved set of reproductive traits related to embryonic development within a uterus and nutrient provisioning through a chorioallantoic placenta [1]. A GEneSTATION user may look up a gene of interest with enriched expression in the placenta and quickly discover that this gene : (i) is often differentially expressed in studies on preeclampsia, a complication of pregnancy characterized by high blood pressure (both of these data types are reported in the ORGANISMAL tab), (ii) originated coincidentally with the placental mammals (reported in the EVOLUTIONARY tab) and (iii) interacts with known pregnancy related genes (reported in the MOLECULAR tab) These associations would suggest that the gene would be a good candidate for further exploration. To facilitate tailored statistical analyses, GEneSTATION makes all data available for easy download in JSON format using the download button on the bottom left of each gene page, analysis page and SynTHy result page

SUMMARY AND FUTURE PERSPECTIVES

MATERIALS AND METHODS