title: Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development.
abstract: Accumulating evidence suggests that noncoding RNAs (ncRNAs) have important regulatory functions. However, lacking of functional annotations for ncRNAs hampered us from carrying out the subsequent functional or predictive research. Here we dissected the expression profiles of 3,458 rat noncoding genes using rat bodymap RNA-sequencing data consisting of 11 solid organs over four developmental stages (juvenile, adolescent, adult and aged) from both sexes, and conducted a comprehensive analysis of differentially expressed noncoding genes (DEnGs) between various conditions. We then constructed a co-expression network between protein-coding and noncoding genes to infer biological functions of noncoding genes. Modules of interest were linked to online databases including DAVID for functional annotation and pathway analysis. Our results indicated that noncoding genes are functionally enriched through pathways similar to those of protein-coding genes. Terms about development of the immune system were enriched with genes from age-related modules, whereas terms about sexual reproduction were enriched with genes in sex-related modules. We also built connection networks on some significant modules to visualize the interactions and regulatory relationship between protein-coding and noncoding genes. Our study could improve our understanding and facilitate a deeper investigation on organ/age/sex-related regulatory events of noncoding genes, which may lead to a superior preclinical model for drug development and translational medicine.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China.|Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wen
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Chen
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.|Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China.
authors.forename: Sibo
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
authors.forename: Jinhang
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.
authors.forename: Yunjie
authors.initials: Y
authors.lastname: Song
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China.
authors.forename: Suqing
authors.initials: S
authors.lastname: Li
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.|Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.|Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China.
authors.forename: Yuanting
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China.
authors.forename: Menglong
authors.initials: M
authors.lastname: Li
mesh_terms: D000367:Age Factors; D000818:Animals; D019295:Computational Biology / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D008297:Male; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D022661:RNA, Untranslated; D051381:Rats; D012737:Sex Factors; D059467:Transcriptome
chemical_list: D022661:RNA, Untranslated