OGEE: an online gene essentiality database

Abstract

OGEE is an Online GEne Essentiality database. Its main purpose is to enhance our understanding of the essentiality of genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. OGEE is freely available at http://ogeedb.embl.de.

Figure 1.

Interface of the ‘Browse’ module.

Figure 2.

Extra gene features shown in a popup window. This window will show up when clicking locus IDs in the ‘Browse’ or ‘Search’ modules.

Figure 3.

Screen shots taken from the ‘Analyze’ module. With integrated tools, the user can easily explore and analyze the collected data, including the visualization of results. Shown here are the results of the following analyses: (A) the proportion of essential genes (P_E) as a function of family size (number of homologous genes within the genome) in mouse, (B) P_E as a function of the earliest expression stage during mouse development, (C) the effects of gene duplication status and involvement in development on gene essentiality in Caenorhabditis elegans and (D) the effects of gene connectivity and involvement in development on gene essentiality in C. elegans.