Bioinformatics analysis reveals the changes of peroxisome proliferator-activated receptor (PPAR) pathway in the development of Marjolin ulcers

Figures & data

Table 1. Descriptive statistics of RNA-seq data.

Sample	Raw reads	Raw bases	Clean reads	Clean bases	Error rate (%)	Q20^a (%)	Q30^b (%)	GC content (%)	Multiple mapped	Uniquely mapped
AB_125914	48738424	7359502024	48451418	7220055275	0.0249	98.15	94.2	52.31	2303006(4.75%)	43086344(88.93%)
AB_702122	50637594	7646276694	50283434	7489620076	0.0252	97.99	93.85	52.26	1908443(3.8%)	46325788(92.13%)
AB_718697	47730986	7207378886	47411482	7072482876	0.0251	98.03	93.94	52	1464905(3.09%)	44059999(92.93%)
AB_720865	52415652	7914763452	52073008	7753408209	0.0249	98.13	94.15	52.11	2880630(5.53%)	45098071(86.61%)
AB_722938	55553030	8388507530	55215120	8235631436	0.0251	98.04	93.94	51.82	1896353(3.43%)	51229213(92.78%)
AB_723158	53328814	8052650914	52996782	7892072112	0.0251	98.04	93.92	51.1	1909449(3.6%)	49040255(92.53%)
ZC_125914	51318286	7749061186	50932278	7602951165	0.0251	98.04	94	52.59	2265978(4.45%)	46385964(91.07%)
ZC_702122	50757772	7664423572	50330206	7482279273	0.0251	98.02	93.94	51.91	2150774(4.27%)	46311272(92.01%)
ZC_718697	52285000	7895035000	51925416	7677151577	0.0264	97.57	92.7	51.62	2094793(4.03%)	46799812(90.13%)
ZC_720865	48981174	7396157274	48572384	7219646457	0.0254	97.92	93.64	51.4	1852065(3.81%)	44912198(92.46%)
ZC_722938	47692856	7201621256	47267918	7037744544	0.0252	98	93.89	52.54	1626878(3.44%)	43774484(92.61%)
ZC_723158	47380890	7154514390	46926272	6973181076	0.0256	97.85	93.53	51.95	2092785(4.46%)	43023225(91.68%)

Note: ^a: Q20, Phred Quality Score 20, probability of incorrect base call 1 in 100;

^b: Q30, Phred Quality Score 30, probability of incorrect base call 1 in 1000.

Samples with name begin with AB are cancer tissue samples, while samples with name begin with ZC are para-cancerous scar tissue samples.

Figure 1. Identification of the Differentially Expressed Genes. A) Volcano plots of differentially expressed genes (DEGs) between the cancer tissues and the para-cancerous scar tissues. The red and green dots indicate the significantly upregulated and downregulated genes, respectively. B) Hierarchical clustering analysis of the DEGs. AB represents the MU tumor tissue samples, while ZC represents the matched para-cancerous scar tissues.

Figure 2. Functional enrichment analysis of the DEGs. A) The top 10 enriched biological processes terms; B) The top 10 enriched cellular component terms; C) The top 10 enriched molecular function terms; D) The top 10 enriched KEGG pathways. The x-axis indicates the number of DEGs, and the y-axis represents the enriched pathways. The adjusted p-value was represented by the color key on the right.

Table 2. The significant enriched top 5 positively and negatively correlated KEGG pathways in GSEA.

Description	setSize	enrichmentScore	NES	pvalue	p.adjust
KEGG_CELL_CYCLE	124	0.632190771	2.3079156	0.0024691	0.015144
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	262	0.534936818	2.1392087	0.0029155	0.0163512
KEGG_PRIMARY_IMMUNODEFICIENCY	35	0.704029322	2.076579	0.0020921	0.015144
KEGG_GRAFT_VERSUS_HOST_DISEASE	37	0.697821921	2.0708643	0.0021186	0.015144
KEGG_P53_SIGNALING_PATHWAY	67	0.617181805	2.0595748	0.002193	0.015144
KEGG_CARDIAC_MUSCLE_CONTRACTION	77	−0.703274411	−2.267061	0.0017921	0.015144
KEGG_DILATED_CARDIOMYOPATHY	90	−0.622646456	−2.056833	0.0017857	0.015144
KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM	83	−0.616946677	−2.000995	0.0018083	0.015144
KEGG_CALCIUM_SIGNALING_PATHWAY	177	−0.550730098	−1.97924	0.0016502	0.015144
KEGG_DRUG_METABOLISM_CYTOCHROME_P450	62	−0.633979472	−1.958604	0.0018416	0.015144

Figure 3. Identification of key pathways and DEGs. A) GSEA enrichment score curves of the four common pathways. The top panel shows the enrichment scores of each pathway. The middle vertical bars display the position of each hit. The bottom panel indicates the ranking metric scores. B) Protein-protein interactions between the important pathways and genes. The different pathways are represented by different big light color ellipses and the hub genes are represented by the small dark color ellipses. The grey lines indicated the associations between the hub genes.

Figure 4. Identification of key pathways and DEGs. A) The diagram of the PPAR signalling pathway. B) The heat map of the DEGs in the PPAR signalling pathway. AB represents the MU tumor tissue samples, while ZC represents the matched para-cancerous scar tissues.

Figure 5. qRT-PCR analysis of the hub genes in the PPAR signalling pathway. GAPDH was used as the reference gene. ** indicates that the gene expression was significantly different between the MU and the para-cancerous scar tissues (p <0.01).

Data availability statement

The raw sequencing data used in this study were deposited in the National Center for Biotechnology Information (NCBI) Sequence ReadArchive (SRA) database with accession number PRJNA821549 (http://www.ncbi.nlm.nih.gov/bioproject/821549). The data for RT-qPCR has been uploaded to 4TU. ResearchData repositories with doi:10.4121/19375049 (https://figshare.com/s/fa15a0a8ef60ee34f0e8).