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.