CanISO

CanISO provides a database of canine (Canis lupus familiaris) genomic and transcriptomic variation derived from whole transcriptome sequencing and whole exome sequencing to support comparative analyses with human GTEx data and cancer research.

Key Features:

• Extensive Transcriptome Data: Contains whole transcriptome sequencing profiles from 157 canine tumors and 64 matched normal tissues, cataloguing 87,692 novel transcript isoforms and 60,992 known isoforms at the gene- and transcript-isoform level.
• Genomic Variation Information: Includes 210,444 unique germline single nucleotide polymorphisms (SNPs) derived from whole exome sequencing of 183 dogs, annotated at gene and transcript levels.
• Query System: Provides a query system for retrieving gene- and transcript-level expression, isoform information, and covered SNPs.
• Comparative Analysis with Human Data: Integrates human GTEx data to enable tissue-level comparisons for identifying tumor-specific gene expression patterns and alternative splicing events between species.

Scientific Applications:

• Canine genomics and transcriptomics: Enables characterization of the canine (Canis lupus familiaris) genome and transcriptome using isoform and variant catalogs.
• Comparative analysis with human data: Facilitates cross-species tissue-level comparisons with GTEx to identify shared or species-specific tumor expression and splicing events.
• Comparative oncology and translational medicine: Supports studies of shared mechanisms of cancer development and progression between dogs and humans.

Methodology:

Whole transcriptome sequencing of 157 canine tumors and 64 matched normal tissues and whole exome sequencing of 183 dogs were used to generate transcript isoform and germline SNP catalogs, which were integrated with human GTEx data for cross-species comparisons.