Comprehensive Developmental Profiles Of Gene Activity In 11 Tissues And 4 Developmental Stages Of A Rat

Though rats are important in the chemical toxicities and drug mechanisms researches, until now, reports describing the function and the regulatory networks across multiple tissues of rats, or their developmental stages have yet been scarce. On the basis of the expression profiles between tissues and developmental stages, in order to further understand the mechanisms of tissue development in rat, we inferred their function networks and regulatory networks from genome-wide gene expression profiles through the module networks method.With the reported rats RNA-Seq data, we catalogued the expression profiles of 26,405 genes,29167 transcripts and 3464 non-coding genes/non-coding RNAs (ncRNAs) annotated in Ensembl. Through comprehensively analysis of the expression of 11 tissues in 4 developmental stages, we predicted 5594 housekeeping genes. On the basis of tissue-specific and stage-specific differentially expressed genes then through further performing GO enrichment analysis and comparative functional analysis of different tissues we observed the correlation degree of the different tissues. Furthermore, we explored growing and aging of different tissues of rats at their different stages. And we had got in total 1272 aging genes including 1401 up-regulated and 232 down-regulated genes. Through comparing samples between different sexes, we figured out sex-biased genes representing hormone metabolic process in gene ontology. Then, we constructed gene co-expression networks for all tissues, indicating that brain, as the most complex tissue, including many DEGs and the most co-expression genes network modules. Meanwhile, based on 1347 transcription factors we selected, we constructed rat regulatory networks in the juvenile and the motif search showed the complexity and diversity of the network. On the basis of regulatory networks, we identified functional modules and explored the molecular mechanisms related to tissue functions. In addition, active factors were also detected in the network, which regulated more than one function module.Our building networks are reliable and informative to understand the biological function of multiple tissues during the development stages in rats, and also provide a framework for the future experimental analyses.