title: Deep sequencing-generated modules demonstrate coherent expression patterns for various cardiac diseases.
abstract: 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.
authors.affiliation: College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea. Electronic address: hse354@gist.ac.kr.
authors.forename: Seong-Eui
authors.initials: SE
authors.lastname: Hong
authors.affiliation: College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea. Electronic address: nkj831130@naver.com.
authors.forename: Kyoung Jin
authors.initials: KJ
authors.lastname: Nho
authors.affiliation: College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea. Electronic address: hksong@gist.ac.kr.
authors.forename: Hong Ki
authors.initials: HK
authors.lastname: Song
authors.affiliation: College of Life Sciences and Systems Biology Research Center, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea. Electronic address: dhkim@gist.ac.kr.
authors.forename: Do Han
authors.initials: DH
authors.lastname: Kim
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D015870:Gene Expression / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks / Q000235:genetics*; D006331:Heart Diseases / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors
keywords: Cardiac function; Gene module; Heart-enriched gene; Next-generation sequencing