iDog

iDog integrates multi-omics data including genomic, transcriptomic, and epigenomic data for domestic dogs (Canis lupus familiaris) and wild canids to support canid research.

Key Features:

• Genomic Variation Data: The resource contains 29.55 million single nucleotide polymorphisms (SNPs) and 16.54 million insertions/deletions (InDels) from 1929 modern samples, plus 29.09 million SNPs from 111 ancient Canis samples.
• Breed-Specific and Disease-Associated Variants: The database includes 43487 breed-specific SNPs and 530 disease/trait-associated variants.
• Gene Expression Data: The platform incorporates data from 141 BioProjects involving gene expression analyses.
• Single-Cell Transcriptomics: A single-cell transcriptome module contains data from 105057 Beagle hippocampus cells.
• Epigenomic Data: An epigenome module evaluates DNA methylation patterns across 547 samples and chromatin accessibility across 87 samples for analysis of gene expression regulation.
• Phenotypic and Genotype-to-Phenotype Data: The resource provides phenotypic data for 897 dog diseases, 3207 genotype-to-phenotype (G2P) pairs, and 349 dog disease-associated genes.
• Ontologies: Two newly constructed ontologies for breed and disease standardization are included.
• Analytical Tools: 13 new analytical tools have been added to the platform.

Scientific Applications:

• Canid Genomic Research: Researchers can access and analyze genomic variation data from modern and ancient canid samples for population genetics and evolutionary studies.
• Disease and Trait Association Studies: The integrated disease/trait-associated variants and genotype-to-phenotype pairs enable investigation of genetic bases of canine diseases and traits.
• Gene Expression Regulation Analysis: DNA methylation and chromatin accessibility data support studies of epigenetic regulation of gene expression in canids.
• Single-Cell Transcriptomics Research: The Beagle hippocampus single-cell data enables cell-type-specific transcriptomic studies in dogs.
• Breed and Disease Standardization: The constructed ontologies support standardized classification and analysis of dog breeds and diseases.

Methodology:

The sources do not provide explicit details on computational methods or algorithms used for data integration, variant calling, or analysis.