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. 2017 Aug 11;18(Suppl 5):554.
doi: 10.1186/s12864-017-3911-3.

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

Giulia Babbi  1 , Pier Luigi Martelli  2 , Giuseppe Profiti  1 , Samuele Bovo  1 , Castrense Savojardo  1 , Rita Casadio  1   3
Affiliations

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

Giulia Babbi et al. BMC Genomics. .

Abstract

Background: Genetic investigations, boosted by modern sequencing techniques, allow dissecting the genetic component of different phenotypic traits. These efforts result in the compilation of lists of genes related to diseases and show that an increasing number of diseases is associated with multiple genes. Investigating functional relations among genes associated with the same disease contributes to highlighting molecular mechanisms of the pathogenesis.

Results: We present eDGAR, a database collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar. For each disease-associated gene, eDGAR collects information on its annotation. Specifically, for lists of genes, eDGAR provides information on: i) interactions retrieved from PDB, BIOGRID and STRING; ii) co-occurrence in stable and functional structural complexes; iii) shared Gene Ontology annotations; iv) shared KEGG and REACTOME pathways; v) enriched functional annotations computed with NET-GE; vi) regulatory interactions derived from TRRUST; vii) localization on chromosomes and/or co-localisation in neighboring loci. The present release of eDGAR includes 2672 diseases, related to 3658 different genes, for a total number of 5729 gene-disease associations. 71% of the genes are linked to 621 multigenic diseases and eDGAR highlights their common GO terms, KEGG/REACTOME pathways, physical and regulatory interactions. eDGAR includes a network based enrichment method for detecting statistically significant functional terms associated to groups of genes.

Conclusions: eDGAR offers a resource to analyze disease-gene associations. In multigenic diseases genes can share physical interactions and/or co-occurrence in the same functional processes. eDGAR is freely available at: edgar.biocomp.unibo.it.

Keywords: Functional enrichment; Gene/disease relationship; Protein functional annotation; Protein-protein interaction.

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Conflict of interest statement

Ethics approval and consent to participate

The authors declare that they used only public data.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Distribution of gene-disease associations. The Y-axis scale is logarithmic. a Number (#) of genes associated with diseases. 2672 diseases are distributed with respect to the number of associated genes. 2051 diseases are monogenic; 621 diseases are associated with multiple genes (from 2 to 69). b Number (#) of diseases associated to genes. 3658 genes are distributed with respect to the number of associated diseases. 2544 genes are associated with a single disease; 1114 genes are associated with multiple diseases (from 2 to 16)
Fig. 2
Fig. 2
Distribution of best IC values of GO terms for genes involved in multigenic diseases. a GO terms shared by genes; b GO terms after enrichment with NET-GE. For each multigenic disease, IC values of gene-associated GO terms (of the three different roots) are evaluated (Eq. 1). In the figure, the highest IC for each disease is shown. The frequency is computed with respect to the total number of multigenic diseases (621). When IC = 0, genes associated with multigenic disease do not share or enrich GO terms (panel a and b respectively)
Fig. 3
Fig. 3
eDGAR page for hypoparathyroidism (OMIM 146200). In the figure, each gene is highlighted with a different color; the Transcription Factor annotation and the known interactions are reported, together with the simple graph describing them. A summary of the KEGG pathways enriched with NET-GE and the shared GO terms for BP is also provided
See this image and copyright information in PMC

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