Molecular Medicine Reports Molecular Medicine Reports 1791-2997 1791-3004 D.A. Spandidos 10.3892/mmr.2016.5349 mmr-14-02-1162 Articles Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3 WangJuan1 CuiChunli2 FuLi3 XiaoZili4 XieNanzi1 LiuYang1 YuLu1 WangHaifeng1 LuoBangzhen1 Department of Geriatric Department of Nephrology, Shanghai Tongji Hospital Affiliated to Tongji University, Shanghai 200065 Department of Dalian Fusheng Natural Pharmaceutical Development Co. Ltd., Dalian, Liaoning 116600 Department of Shanghai Jinfang Biotechnology Co. Ltd., Shanghai 201210, P.R. China Correspondence to: Dr Chunli Cui, Department of Nephrology, Shanghai Tongji Hospital Affiliated to Tongji University, 389 Xincun Road, Putuo, Shanghai 200065, P.R. China, E-mail: tjchunlicui@126.com Mr. Li Fu, Dalian Fusheng Natural Pharmaceutical Development Co. Ltd., 5 Tieshan Road, Dalian, Liaoning 116600, P.R. China, E-mail: lifudalian@126.com 08 2016 27 05 2016 14 2 1162 1172 14 05 2015 19 04 2016 Copyright: © Wang et al. 2016 This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Diabetic nephropathy (DN), a common diabetes-related complication, is the leading cause of progressive chronic kidney disease (CKD) and end-stage renal disease. Despite the rapid development in the treatment of DN, currently available therapies used in early DN cannot prevent progressive CKD. The exact pathogenic mechanisms and the molecular events underlying DN development remain unclear. Ginsenoside Rg3 is a herbal medicine with numerous pharmacological effects. To gain a greater understanding of the molecular mechanism and signaling pathway underlying the effect of ginsenoside Rg3 in DN therapy, an RNA sequencing approach was performed to screen differential gene expression in a rat model of DN treated with ginsenoside Rg3. A combined bioinformatics analysis was then conducted to obtain insights into the underlying molecular mechanisms of the disease development, in order to identify potential novel targets for the treatment of DN. Six Sprague-Dawley male rats were randomly divided into 3 groups: Normal control group, DN group and ginsenoside-Rg3 treatment group, with two rats in each group. RNA sequencing was adopted for transcriptome profiling of cells from the renal cortex of DN rat model. Differentially expressed genes were screened out. Cluster analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to analyze the differentially expressed genes. In total, 78 differentially expressed genes in the DN control group were identified when compared with the normal control group, of which 52 genes were upregulated and 26 genes were downregulated. Differential expression of 43 genes was observed in the ginsenoside-Rg3 treatment group when compared with the DN control group, consisting of 10 upregulated genes and 33 downregulated genes. Notably, 21 that were downregulated in the DN control group compared with the control were then shown to be upregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. In addition, 7 upregulated genes in the DN control group compared with the control were then shown to be downregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. Cluster analysis based on differentially expressed genes indicated that the transcriptomes are quite different among the samples. Distinct GO terms associated with these groups of genes were shown to be enriched. KEGG pathway analysis demonstrated that differentially expressed genes were predominantly involved in the fatty acid metabolism pathway and peroxisome proliferator-activated receptor (PPAR) signaling pathway. To the best of our knowledge, this study was the first to present whole genome expression profiling in DN with ginsenoside-Rg3 treatment by RNA-Seq. A set of differentially expressed genes and pathways were identified. These data provided an insight into understanding the molecular mechanisms underlying the effect of ginsenoside-Rg3 treatment of DN.

 diabetic nephropathy ginsenoside Rg3 RNA-Seq bioinformatics analysis Introduction

Diabetic nephropathy (DN) is a chronic microvascular complication of type 1 and type 2 diabetes mellitus and is the leading cause of progressive chronic kidney disease and end-stage renal disease, which puts a serious burden on the patient's family and on society (1).

The exact pathogenic mechanisms and the molecular events of DN remain unclear. Evidence suggests that environmental and genetic factors are involved in the development of DN (2). A number of factors are known to be critical in the development of DN, such as insulin-like growth factor 1 (IGF1), transforming growth factor beta, platelet-derived growth factor (PDGF), fibroblast growth factor (FGF), interleukins (ILs), tumor necrosis factor-α (TNF-α), vascular endothelial growth factor (VEGF) and endothelin (3). These factors effect processes including glucose metabolism, renal hemodynamics, cell matrix metabolism, cell proliferation, cell hypertrophy, cell apoptosis, abnormal angiogenesis and cytokine-mediated inflammatory response, which are involved in DN pathogenesis. Searching for agents that regulate the expression of these cytokines to intervene and prevent the development of DN an area of research.

Ginsenoside Rg3 is an active ingredients in Ginseng, which can inhibit the growth and metastasis of tumors through the downregulation of VEGF, bFGF gene expression and inhibiting the formation of abnormal new blood vessels. Besides, ginsenoside Rg3 has a number of pharmacological effects, including the inducing the apoptosis of tumor cells, promoting T lymphocyte mitosis and NK cell activity, stimulating the phagocytic function of the reticuloendothelial system, promoting the secretion of B lymphocyte antibodies, promoting antiplatelet aggregation to prevent thrombosis, dilating the blood vessels and increasing blood supply (4,5).

Therefore, it was hypothesized that ginsenoside Rg3 could prevent the occurrence and development of DN by effecting the gene expression and regulation of various cytokines to delay the progression of DN to end-stage renal failure. To the best of our knowledge, this study was the first to observe the effect of ginsenoside Rg3 on the changes of the gene expression profile in DN rats, which may aid in the identification of novel targets for the treatment of DN.

 Materials and methods Animal group

Six male Sprague-Dawley (SD) rats were provided by Shanghai Laboratory Animal Center (Shanghai, China) (average weight, 300 g). The rats were divided randomly into three groups: Control group (sample ID: 1 and 3), DN control group (sample ID: 8 and 9) and ginsenoside-Rg3 treatment group (sample ID: 15 and 16), with two rats in each group.

 Modeling and Rg3 drugs

The normal control group was given normal feed. The DN control and ginsenoside-Rg3 treatment groups were administered a high lipid diet for two months, then were treated with intraperitoneal injection of streptozotocin (STZ; 45 mg/kg) induced diabetic nephropathy. After the models were established, the ginsenoside-Rg3 treatment group were administered Rg3 (0.5 mg/kg) once a day for 30 days.

 RNA extraction

Samples from renal cortex were collected and stored in liquid nitrogen at −80°C until RNA extraction was performed. Total RNA was extracted from the samples of renal cortex using TRIzol reagent (Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer's instructions. RNA quantity and quality were measured using the NanoDrop ND-1000 spectrophotometer and Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA).

 RNA-seq data generation

RNA-seq libraries were prepared in accordance with Illumina's sample preparation protocol. The libraries were sequenced onto an Illumina HiSeq2000 instrument (Illumina Inc., San Diego, CA, USA) and subjected to 100 cycles of paired end (2×100 bp) sequencing. The processing of fluorescent images into sequences, base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8). Prior to assembly, high-quality clean reads were generated using FASTX toolkit pipeline (version 0.0.13), then the resulting high-quality reads were mapped onto the UCSC (mm10) using Tophat (version: 2.0.6) (6). Cufflink (version: 2.0.2) (7) was used to process the Tophat alignments. Additionally, transcript expression levels were estimated using Fragments Per Kilobases per Million reads (FPKM) values. Finally, the program Cuffdiff was used to define differentially expressed genes as a gene set for further analysis. The selection criteria of differentially expressed genes was based upon the fold-changes of the expression levels (P<0.05). If the gene expression status was consistent in two comparison groups (DN control group vs. the normal control group including sample ID1 vs. ID8 and sample ID3 vs. ID9; ginsenoside-Rg3 treatment group vs. DN control group including sample ID8 vs. ID15 and sample ID9 vs. ID16), they were defined as differentially expressed genes. All analyses were performed at Shanghai Biotechnology Corporation (Shanghai, China).

 Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses

In order to examine the biological significance of the differentially expressed genes, the GO and KEGG (http://www.genome.jp/kegg/) pathway analysis produced by Kanehisa Laboratories (Kyoto, Japan) were performed to investigate their functional and pathway annotation (8,9). GO and pathway analyses were conducted using TargetMine (available at http://targetmine.nibio.go.jp/) based on a hypergeometric test (10).

 Results Differentially expressed genes generated by RNA-Seq Normal control group and DN control group

Totally, 78 differentially expressed genes in the DN control group were identified compared with the normal control group. Of these, 52 genes were upregulated while 26 genes were downregulated. The top ten enriched differentially expressed genes based on fold-change are listed in Table I.

 DN control group and ginsenoside-Rg3 treatment group

In total, 43 differentially expressed genes in the ginsenoside-Rg3 treatment group were identified compared with the DN control group. Of these, 10 genes were upregulated while 33 genes were downregulated. The top ten enriched differentially expressed genes based on fold-change are listed in Table II.

 Bioinformatics analysis

In total, 21 genes that were downregulated in the DN control group compared with the normal control group, were found to be upregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. In addition, upregulation of 7 genes in the DN control group compared with the normal control group were downregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. These 28 differentially expressed genes are shown in Table III.

 Cluster analysis

To obtain a global view of the differentially expressed genes, the hierarchical cluster was performed among the samples. The heat maps indicated that the transcriptomes are different (Figs. 1–3).

 GO and KEGG analysis

KEGG analysis was performed on the differentially expressed genes in the DN control group compared with the normal control group and in the ginsenoside-Rg3 treatment group compared with the DN control group, respectively. Significantly affected pathways were identified in the upregulated gene sets in the normal control compared with the DN control group, and also in the downregulated gene sets in the DN control compared with the ginsenoside-Rg3 treatment group (Table IV).

The pathways, including peroxisome PPAR signaling pathway, mineral absorption and fatty acid degradation, may be critical in ginsenoside-Rg3 treatment of DN, implicating certain key genes enriched by these pathways (such as Acaala and Acaalb) as potential therapeutic targets.

To gain a greater understanding of the biological implications, GO enrichment analysis on differentially expressed genes was performed. GO is a standardized gene functional classification system, which provides a strictly defined concept and controlled vocabulary to describe properties of genes and their products. GO-annotated differentially expressed genes predominantly belong to the three functional clusters (biological process, cellular component and molecular function). Enrichment analysis focused on the 28 differentially expressed genes (21 upregulated genes and 7 downregulated genes) following administration of ginsenoside-Rg3. It was demonstrated that the 28 differentially expressed genes in the cluster of biological process was predominantly associated with lipid metabolism process (Table V). In addition, KEGG enrichment analysis was also performed on the 28 genes. Five pathways, including the PPAR signaling pathway, fatty acid degradation, nitrogen metabolism, proximal tubule bicarbonate reclamation and valine, leucine and isoleucine degradation were shown to be enriched (Table VI).

 Pathway analysis

Differentially expressed genes were mapped to rno00071 and rno03320 pathways of KEGG to observe the gene distribution and effects. In the rno00071 pathway, it was demonstrated that ginsenoside-Rg3 treatment reversed the expression of the acyl-CoA dehydrogenase, short/branched chain gene, acetyl-CoA acyltransferase, enoyl-CoA hydratase/3-hydroxyacyl CoA dehydrogenase and cytochrome P450 family 4 subfamily a polypeptide 2, suggesting a critical role of fatty acid metabolism pathway through affecting the four key genes in the process of DN with ginsenoside-Rg3 treatment (Figs. 4 and 5). In the rno03320 pathway, change in the expression of five genes: HMGCS2, APoCii, CYP4A1, ThinoleseB, PEPCK in DN was reversed by treatment with ginsenoside-Rg3 (Figs. 6 and 7).

 Discussion

Recently, the revolution of next generation sequencing (NGS) has had a great impact on genome research. RNA sequencing (RNA-Seq) is an innovative NGS tool for the comprehensive transcriptome profiling on a genome-wide scale using deep-sequencing technologies (11,12). Studies using this tool have already altered perception on the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms (11). In contrast to the technologies of microarray and qPCR analysis, RNA-seq allows for the identification of novel transcripts, examination of all RNA species, and identification of alternative splicing and mutations (13).

The present study collected renal cortex samples of six rats (n=2/group), which were classified into the normal control group, DN control group and ginsenoside-Rg3 treatment group. Gene expression profiling analysis was performed using an NGS strategy with the aim of identifying biomarker genes relevant to the molecular pathogenesis of DN. In total, there were 78 differentially expressed genes in the DN control group when compared with the normal control group, of which 52 genes were upregulated and 26 genes were downregulated. Expression of 43 genes was differentially regulated in the ginsenoside-Rg3 treatment group when compared with the DN control group, consisting of 10 upregulated and 33 genes downregulated. Notably, 21 downregulated genes in the DN control group were upregulated in the ginsenoside-Rg3 treatment group, and 7 upregulated genes in the DN control group were downregulated in the ginsenoside-Rg3 treatment group. GO annotation analysis showed that the differentially expressed genes were predominantly associated with the lipid metabolism process. KEGG pathway enrichment analysis showed that fatty acid degradation and PPAR signaling pathways were associated with the differentially expressed genes.

Recently, lipid metabolism disorder has become a focus of research in the pathogenesis of DN. Disordered lipid metabolism and renal lipid accumulation are not only associated with obesity-related renal disease and DN, but they may also contribute to the disease process (14). Sustained hyperglycemia in diabetes promotes fatty acid (FA) synthesis and triacylglycerol (TG) accumulation. Elevated serum TG, free FAs (FFAs), and modified cholesterol cause ectopic lipid accumulation in nonadipose tissues, leading to lipotoxicity (15), which may be involved in the pathogenesis of DN (16). Herman-Edelstein et al (17) investigated the association of altered renal TG and cholesterol metabolism with lipid accumulation in patients with DN. The results showed a highly significant correlation between glomerular filtration rate, inflammation and lipid metabolism associated genes, suggesting a potential role of abnormal lipid metabolism in the pathogenesis of DN (17).

PPAR is a member of the nuclear hormone receptor superfamily and is critical in lipid metabolism (18). PPAR is highly expressed in various organs, such as the liver, renal cortex and heart. Knocking out PPARα appeared to aggravate the severity of DN through an increase in extracellular matrix formation, inflammation, and circulating FFA and TG concentrations (19). PPAR-γ is the most extensively studied PPAR subtype and is involved in adipocyte differentiation, and glucose and lipid metabolism. The mechanisms of PPAR-γ in DN remain to be fully elucidated. A study suggested PPAR-γ has an important role in regulating insulin sensitivity (20). Gene polymorphisms of PPAR-γ gene polymorphism Ala12 carriers exhibited an improvement in insulin sensitivity (21), and may be responsible for the development of DN.

Current therapeutic strategies for DN remain suboptimal and are directed at delaying disease progression, for example, intensive glucose and blood pressure control, dyslipidemia and lipid-lowering drugs. Ginsenoside Rg3, an active component of Panax ginseng, has been identified to have a protective effect against hyperglycemia, obesity and diabetes in vivo (22). Animal experiments demonstrated the effect of ginsenoside Rg3 on diabetic renal damage (23). However, the precise mechanisms of these actions remain to be fully elucidated. Hwang et al (24) investigated the molecular basis of ginsenoside Rg3. Their results found that the effect of ginsenoside Rg3 in inhibiting adipocyte differentiation, and also PPAR-γ signaling was involved in the inhibition of adipocyte differentiation by ginsenoside Rg3 (24). Ginsenoside has been shown to exhibit anti-obesity and anti-hyperglycemia effects that involve the PPAR mediated pathway (25). Sun et al (26) investigated the effect of ginsenoside Rg3 on the expression of VEGF and TNF-α in the retina of diabetic rats, and demonstrated that ginsenoside Rg3 could downregulate the expression of VEGF and TNF-α, which may disrupt the development of diabetic retinopathy. Kang et al (22) analyzed the effect of ginsenoside Rg3 on the progression of renal disease in type II diabetic rat models, and provided evidence that Rg3 can prevent the progression of renal damage and dysfunction of diabetic rats. Lee et al (27) evaluated the effects of ginsenoside Rg3 on glucose uptake and the glucose transport system in mature 3T3-L1 cells, and demonstrated that ginsenoside Rg3 may stimulate the expression of insulin receptor substrate expression and phosphatidylinositol 3-kinase-110a protein, which may therefore be a valuable antidiabetic and antihyperglycemic agent. Bu et al (15) also demonstrated similar effects of ginsenoside Rg3 in reducing the fasting blood glucose level, reducing food and water intake, improving oral glucose tolerance, and repairing injured pancreas tissues of alloxan-induced diabetic mice. These studies suggest that ginsenoside Rg3 has potential for clinical use in preventing and treating diabetes and its complications. The present study also suggested that ginsenoside Rg3 may be used as a novel and useful adjunctive drug for the treatment of DN.

High throughput RNA-Seq technology allows comprehensive transcriptome profiling. A set genes were identified to be differentially expressed following ginsenoside Rg3 treatment. Gene set enrichment analyses identified the specific biological processes, predominantly lipid/fatty acid metabolism and the PPAR signaling pathway, were associated with these genes. The identification of these genes and pathway analyses have provided novel insights into the molecular mechanisms underlying the effect of ginsenoside-Rg3 on DN. As the sample sizes in the present study are small, these findings require further validation.

 Acknowledgments

This study was supported by the Enterprise postdoctoral fund in Liaoning province (grant no. 106561).

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Hierarchical clustering of differentially expressed genes in the DN control group compared with the normal control group. Each row represents a differentially expressed gene, while each column represents a sample. In the heatmap, green represents genes that are downregulated and red represents genes that are upregulated.

Hierarchical clustering of differentially expressed genes in the ginsenoside-Rg3 treatment group compared with the DN control group. Each row represents a differentially expressed gene, while each column represents a sample. In the heatmap, green represents genes that are downregulated and red represents genes that are upregulated.

Hierarchical clustering of differentially expressed genes among six samples. Each row represents a differentially expressed gene, while each column represents a sample. In the heatmap, green represents genes that are downregulated red represents genes that are upregulated.

Differentially expressed gene distribution in the rno00071 pathway. Differentially expressed genes in the DN control group compared with the normal control group were shown to be associated with fatty acid degradation. Bright green, upregulated genes; red, downregulated genes; pale green, species specific genes.

Differentially expressed gene distribution in the rno00071 pathway. Differentially express genes in the ginsenoside-Rg3 treatment group compared with the DN control group were shown to be associated with fatty acid degradation. Bright green, upregulated genes; red, downregulated genes; pale green, species specific genes.

Differentially expressed gene distribution in the rno03320 pathway. Differentially express genes in the DN control group compared with the normal control group were shown to be associated with the PPAR signaling pathway. Red, downregulated genes; pale green, species specific genes. PPAR, peroxisome proliferator-activated receptor.

Differentially expressed gene distribution in rno03320 pathway. Differentially expressed genes in the in the ginsenoside-Rg3 treatment group compared with the DN control group were shown to be associated with the PPAR signaling pathway. Bright green, upregulated genes; pale green, species specific genes. PPAR, peroxisome proliferator-activated receptor.

Top ten enriched differentially expressed genes in the DN control group compared with the normal control group.

Gene Description
Upregulated
 Angptl4 Angiopoietin-like 4
 Hmgcs2 3-Hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
 Havcr1 Hepatitis A virus cellular receptor 1
 Gpx2 Glutathione peroxidase 2
 Slc25a25 Solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25
 Rarres2 Retinoic acid receptor responder (tazarotene induced) 2
 Spp1 Secreted phosphoprotein 1
 Serhl2 Serine hydrolase-like 2
 Eci1 Enoyl-CoA Δ isomerase 1
 Apoc2 Apolipoprotein C-II
Downregulated
 LOC361914 Similar to solute carrier family 7 (cationic amino acid transporter, y+system), member 12
 Cacng5 Calcium channel, voltage-dependent, γ subunit 5
 Slc7a12 Solute carrier family 7 (cationic amino acid transporter, y+system), member 12
 LOC686288 Similar to olfactory receptor Olr1668
 Prima1 Proline rich membrane anchor 1
 Slco1a6 Solute carrier organic anion transporter family, member 1a6
 RT1-CE1 RT1 class I, locus1
 Hnmt histamine N-methyltransferase
 Cyp2c11 Cytochrome P450, subfamily 2, polypeptide 11
Cyp2c24 Cytochrome P450, family 2, subfamily c, polypeptide 24

Top ten enriched differentially expressed genes in the ginsenoside-Rg3 treatment group compared with the DN control group.

Gene Description
Upregulated
 Cyp2c24 Cytochrome P450, family 2, subfamily c, polypeptide 24
 Gtpbp4 GTP binding protein 4
 Prima1 Proline rich membrane anchor 1
 Slco1a6 Solute carrier organic anion transporter family, meber 1a6
 Prlr Prolactin receptor
 Tmem72 Transmembrane protein 72
 Acadsb Acyl-CoA dehydrogenase, short/branched chain
 Ppm1k Protein phosphatase, Mg2+/Mn2+ dependent, 1K
 LOC100365744 Hypothetical protein LOC100365744
 Slc30a1 Solute carrier family 30 (zinc transporter, membrane 1
Downregulated
 Havcr1 Hepatitis A virus cellular receptor 1
 Ril Reversion induced LIM gene
 Hmgcs2 3-Hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
 Slc25a25 Solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25
 Cxcl11 Chemokine (C-X-C motif) ligand 11
 Acaa1b Acetyl-Coenzyme A acyltransferase 1B
 Resp18 Regulated endocrine-specific protein 18
 Rarres2 Retinoic acid receptor responder (tazarotene induced) 2
 Rbp1 Retinol binding protein 1, cellular
 Gdf15 Growth differentiation factor 15

Twenty-eight differentially expressed genes.

Gene name Description
LOC100365744 Hypothetical protein LOC100365744
Ppm1k Protein phosphatase, Mg2+/Mn2+ dependent, 1K
Acadsb Acyl-CoA dehydrogenase, short/branched chain
Slco1a6 Solute carrier organic anion transporter family, member 1a6
Prlr Prolactin receptor
Cyp2c24 Cytochrome P450, family 2, subfamily c, polypeptide 24
Prima1 Proline rich membrane anchor 1
Hmgcs2 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
Eci1 Enoyl-CoA Δ isomerase 1
Gdf15 Growth differentiation factor 15
Plin2 Perilipin 2
Slc25a25 Solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25
Havcr1 Hepatitis A virus cellular receptor 1
Acaa1a Acetyl-Coenzyme A acyltransferase 1A
Ephx1 Epoxide hydrolase 1, microsomal
Pck1 Phosphoenolpyruvate carboxykinase 1 (soluble)
Car15 Carbonic anhydrase 15
Apoc3 Apolipoprotein C-III
Ddit4l DNA-damage-inducible transcript 4-like
Ril Reversion induced LIM gene
Cyp4a1 Cytochrome P450, family 4, subfamily a, polypeptide 1
Rbp1 Retinol binding protein 1, cellular
Mt1a Metallothionein 1a
Car4 Carbonic anhydrase 4
Gpx1 Glutathione peroxidase 1
Bhmt Betaine-homocysteine S-methyltransferase
Rarres2 Retinoic acid receptor responder (tazarotene induced) 2
Resp18 Regulated endocrine-specific protein 18

KEGG enrichment analysis of differential expressed genes.

Group ID Pathway P-value Count Genes
Normal control vs. DN control group rno03320 PPAR signaling pathway 4.09253×10−5 7 Acaa1a, Angptl4, Apoc3, Cyp4a1, Cyp4a3, Hmgcs2, Pck1
rno04978 Mineral absorption 0.00179 5 Fth1, Mt1a, Mt2A, S100g, Tf
rno00071 Fatty acid degradation 0.00199 5 Acaa1a, Acaa2, Cyp4a1, Cyp4a3, Eci1
DN control vs. ginsenoside-Rg3 treatment group rno03320 PPAR signaling pathway 5.51233×10−5 6 Acaa1a, Acaa1b, Apoc3, Cyp4a1, Hmgcs2, Pck1
rno00071 Fatty acid degradation 0.00908 4 Acaa1a, Acaa1b, Cyp4a1, Eci1

GO analysis on 28 differentially expressed genes.

Ontology GO ID Term P-value Genes
GO_BP GO:0006641 Triglyceride metabolic process 0.00194 GPX1, APOC3, PCK1
GO_BP GO:0006639 Acylglycerol metabolic process 0.00242 GPX1, APOC3, PCK1
GO_BP GO:0006638 Neutral lipid metabolic process 0.00260 GPX1, APOC3, PCK1
GO_BP GO:0006720 Isoprenoid metabolic process 0.00260 RARRES2, HMGCS2, RBP1
GO_BP GO:0006662 Glycerol ether metabolic process 0.00269 GPX1, APOC3, PCK1
GO_BP GO:0018904 Organic ether metabolic process 0.00287 GPX1, APOC3, PCK1
GO_BP GO:0009636 Response to toxin 0.00335 GPX1, MT1A, EPHX1
GO_BP GO:0009725 Response to hormone stimulus 0.00380 GPX1, HMGCS2, APOC3, CAR4, PCK1
GO_BP GO:0010033 Response to organic substance 0.00563 GPX1, HMGCS2, APOC3, EPHX1, CAR4, PCK1
GO_BP GO:0009719 Response to endogenous stimulus 0.00576 GPX1, HMGCS2, APOC3, CAR4, PCK1
GO_BP GO:0046486 Glycerolipid metabolic process 0.01784 GPX1, APOC3, PCK1
GO_MF GO:0046914 Transition metal ion binding 0.02858 RIL, CYP4A1, MT1A, BHMT, CYP2C24, CAR4, PCK1
GO_BP GO:0007584 Response to nutrient 0.02963 GPX1, HMGCS2, APOC3
GO_BP GO:0043434 Response to peptide hormone stimulus 0.03400 HMGCS2, APOC3, PCK1
GO_MF GO:0009055 Electron carrier activity 0.03467 ACADSB, CYP4A1, CYP2C24
GO_BP GO:0009410 Response to xenobiotic stimulus 0.03516 GPX1, EPHX1
GO_BP GO:0016101 Diterpenoid metabolic process 0.03899 RARRES2, RBP1
GO_BP GO:0001523 Retinoid metabolic process 0.03899 RARRES2, RBP1
GO_BP GO:0006721 Terpenoid metabolic process 0.04281 RARRES2, RBP1
GO_BP GO:0055114 Oxidation reduction 0.04416 GPX1, ACADSB, CYP4A1, CYP2C24

GO_BP, biological process GO_MF, molecular function.

KEGG enrichment analysis on 28 differentially expressed genes.

Pathway Term P-value Count Genes
rno03320 PPAR signaling pathway 7.88382×10−8 5 Acaa1a,Apoc3, Cyp4a1, Hmgcs2, Pck1
rno00071 Fatty acid degradation 4.42130×10−5 3 Acaa1a, Cyp4a1, Eci1
rno00910 Nitrogen metabolism 0.00029 2 Car15, Car4
rno04964 Proximal tubule bicarbonate reclamation 0.00049 2 Car4, Pck1
rno00280 Valine, leucine and isoleucine degradation 0.00286 2 Acaa1a, Hmgcs2