Deep sequencing-generated modules demonstrate coherent expression patterns for various cardiac diseases

• The present study attempted to identify the heart-enriched genes based on next-generation sequencing data.
• The gene modules sensitive to various cardiac disease-related perturbations were investigated.
• We identified seven gene modules and related transcription factors associated with various cardiac diseases.
• Our study could contribute to the classification of heart-enriched genes and modules for cardiac pathogenesis.

As sequencing technology rapidly develops, gene annotations have also become increasingly sophisticated with incorporation of information regarding the temporal–spatial context of alternative splicing patterns, developmental stages, and tissue specificity. The present study aimed to identify the heart-enriched genes based on next-generation sequencing data and to investigate the gene modules demonstrating coherent expression patterns for various cardiac disease-related perturbations. Seven gene modules, including 382 heart-enriched genes, were identified. At least two modules containing differentially expressed genes were experimentally confirmed to be highly sensitive to various cardiac diseases. Transcription factors regulating the gene modules were then analyzed based on knowledgebase information; the expression of eight transcription factors changed significantly during pressure-overload cardiac hypertrophy, suggesting possible regulation of the modules by the identified transcription factors. Collectively, our results contribute to the classification of heart-enriched genes and their modules and would aid in identification of the transcription factors involved in cardiac pathogenesis in the future.