Defining differentially expressed genes (DEGs) at different degrees
Through the analysis of skin transcriptome sequencing data, 228 differentially expressed genes were obtained by comparing P_S with NP_S, including 126 up-regulated genes and 102 down-regulated genes (Fig 1 A; Fig 1 C). P_B compared with NP_B, 86 differentially expressed genes were obtained, including 71 up-regulated genes and 15 down-regulated genes (Fig 1 B; Fig 1 D) .
Functional annotation and classification of theDEGs
Public databases (NR, Swiss-Prot, KOG, COG, Pfam, GO, and KEGG) were used to annotate the DEGs. DEGs in skin Gene Ontology (GO) annotation showed that the obtained DEGs were classified into 10, 7 and 3 functional subcategories for biological process, cellular component and molecular function, respectively (Fig 2 A). Many genes were classified into more than one sub-category. The GO category of biological process showed a high percentage of cellular process, single-organism process. In terms of cellular component cell part and cell were high. With regard to molecular function, the top two GO terms were catalytic activity, binding. DEGs in brain Gene Ontology (GO) annotation showed that the obtained DEGs were classified into 9, 6 and 5 functional subcategories for biological process, cellular component and molecular function, respectively (Fig 2 B). Many genes were classified into more than one sub-category. The GO category of biological process showed a high percentage of cellular process. In terms of cellular component cell part, cell and organelle were high. With regard to molecular function, the top GO terms were binding.
DEGs in skin COG annotations showed that assigned to 24 COG categories (Fig 3 A). Among these functional categories, lipid transport and metabolism the largest group (4 DEGs) followed by amino acid transport and metabolism(3), translation, ribosomal structure and biogenesis (3), posttranslational modification, protein turnover, chaperones (3), general function prediction only(3). The smaller groups were nucleotide transport and metabolism (1), coenzyme transport (1) and transcription (1). DEGs in brain COG annotations showed that assigned to 24 COG categories (Fig 3 B). Among transcription (1), general function prediction only is the tow largest group (2 DEGs) followed by energy production and conversion (1), function unknown (1).
To further identify the biological pathways activated in skin, DEGs pathways were identified using the KEGG database (Fig 4 A). The KEGG pathway analysis showed 126 DEGs mapped into five major pathways: cellular process, environmental information processing, genetic information processing, metabolism, human diseases and organismal systems. Among the 37 biochemical pathways, the top three enriched pathways were signal transduction (17), immune system(15) and signaling molecules and interaction(12). Meanwhile, enriched pathways related to lipid metabolism and cellular community-eukaryotes were also found in the metabolism pathway. In addition, to further identify the biological pathways activated in brain, DEGs pathways were identified using the KEGG database (Fig 4 B). The KEGG pathway analysis showed 108 DEGs mapped into five major pathways: cellular process, environmental information processing, genetic information processing, metabolism, human diseases and organismal systems. Among the 29 biochemical pathways, the top three enriched pathways were signal transduction (12), nervous system(10) and cancers: overview (11). Meanwhile, enriched pathways related to signaling molecules and interaction.