Identification of potential key molecules and signaling pathways for psoriasis based on weighted gene co-expression network analysis

Table 1 Details of five datasets

GEO ID	Samples, Normal:Case	Platforms	Author	Type	Source
GSE13355	64:58	GPL570	Gudjonsson JE	mRNA	Skin
GSE66511	12:12	GPL12688	Keermann M	mRNA	Skin
GSE145054	4:4	GPL19117	Mildner M	miRNA	Skin
GSE142582	5:5	GPL20301	Yu Z	miRNA	Skin
GSE129373	9:9	GPL11154	Srivastava A	miRNA	Skin

Table 2 Clinical information of healthy control individuals and patients with psoriasis in vitro validation

Group	Sample number	Sampling location	Sex	Age	Height, cm	Body weight, kg	BMI	Smoking	Drinking	History of ASCVD	History of hypertension	History of hyperlipidemia	History of diabetes	Psoriatic arthritis	Severity index, PASI	Whether to collect non-lesion parts
Normal control group	C1	Right forearm extension side	Female	47	158	54	21.6	No	No	No	No	No	No
	C2	Right sole of the foot	Male	60	178	70	22.1	Yes	Yes	No	No	No	No
	C3	Left sole of the foot	Male	59	183	81	24.2	No	No	No	No	No	No
	C4	Left armpit	Female	27	160	52	20.3	No	Yes	No	No	No	No
	C7	Left forearm extension side	Female	18	160	50	19.5	No	No	No	No	No	No
	C9	Right shoulder	Female	27	161	62	23.9	No	No	No	No	No	No
	C11	Right calf	Female	60	156	55	22.6	No	No	No	No	No	No
Psoriasis group	E2-2	Right forearm	Male	19	177	58	18.5	No	No	No	No	No	No	No	10.5	Yes
	E3-2	Back	Female	58	157	58	23.5	No	No	No	No	Yes	No	No	8	Yes
	E5-2	Left calf stretched side	Male	55	176	68	22	No	No	No	Yes	No	Yes	No	13.4	Yes
	E6-2	Outer left thigh	Female	44	166	67	24.3	No	No	No	No	No	No	No	11.9	Yes
	E7-2	Right thigh internal test	Male	62	170	66	22.8	Yes	No	No	No	No	No	No	8.6	Yes
	E8-2	Right forearm extension side	Male	48	170	58	20.1	Yes	No	No	No	No	No	No	15.4	Yes
	E10-2	Back	Male	18	172	60	20.3	Yes	No	No	No	No	No	No	22.2	Yes

ASCVD: Arteriosclerotic cardiovascular disease; BMI: Body mass index.

Table 3 Kyoto Encyclopedia of Genes and Genomics function enrichment of differentially expressed mRNAs

Category	hsa	Term	Count	P value	Genes
KEGG_PATHWAY	hsa03320	PPAR signaling pathway	14	3.07E-06	GK, MMP1, ADIPOQ, LPL, FADS2, ACADL, ACOX2, FABP5, FABP7, ACSBG1, PLIN1, ANGPTL4, SLC27A4, PPARD
KEGG_PATHWAY	hsa05164	Influenza A	22	1.05E-05	NLRX1, RSAD2, DDX58, STAT1, TMPRSS4, MX1, MAPK13, PYCARD, CXCL10, SOCS3, OAS1, OAS2, IL-1B, OAS3, TNFSF10, IRF7, CCL2, PRSS3, KPNA2, PRSS2, MYD88, IRF9
KEGG_PATHWAY	hsa05133	Pertussis	12	2.56E-04	PYCARD, C1QB, CASP7, NOS2, CALML5, IL-1B, IRF1, IRF8, CALML3, FOS, MYD88, MAPK13
KEGG_PATHWAY	hsa05162	Measles	16	4.14E-04	DDX58, STAT1, MX1, CD3G, CD3D, OAS1, CCNE2, CCNE1, OAS2, IL-1B, OAS3, TNFSF10, IRF7, PRKCQ, MYD88, IRF9
KEGG_PATHWAY	hsa04668	TNF signaling pathway	14	4.87E-04	MLKL, CCL20, CXCL1, FOS, NOD2, SELE, MMP9, MAPK13, CXCL10, SOCS3, CASP7, IL-1B, CCL2, JUNB
KEGG_PATHWAY	hsa04062	Chemokine signaling pathway	19	7.44E-04	LYN, CXCL9, CCL22, STAT1, CCL20, CXCR4, CXCL1, CXCL13, CXCL10, HCK, CCL8, PLCB4, CXCR2, RAC2, CCL2, CCR7, CCL19, CCL18, CCL27
KEGG_PATHWAY	hsa04060	Cytokine-cytokine receptor interaction	21	0.002838	CXCL9, IL20, IL4R, CCL22, CCL20, CXCR4, IL19, CXCL1, CXCL13, CXCL10, CCL8, IL-1B, CXCR2, TNFSF10, CCL2, CCR7, CCL19, IL7R, CCL18, CCL27, TNFRSF21
KEGG_PATHWAY	hsa05160	Hepatitis C	14	0.003635	DDX58, STAT1, IFIT1, CLDN1, MAPK13, SOCS3, OAS1, OAS2, IRF1, OAS3, CLDN8, IRF7, CLDN17, IRF9
KEGG_PATHWAY	hsa00590	Arachidonic acid metabolism	9	0.003655	PLA2G2F, HPGDS, GPX2, PLA2G4D, PLA2G2A, PLA2G3, ALOX12B, CYP2E1, CYP4F8
KEGG_PATHWAY	hsa04110	Cell cycle	13	0.00555	BUB1B, TTK, CDC6, CDC25B, CCNA2, CDC20, CCNB2, CCNB1, CCNE2, PTTG1, CCNE1, CDK1, MAD2L1
KEGG_PATHWAY	hsa05142	Chagas disease (American trypanosomiasis)	11	0.011418	C1QB, GNA15, PLCB4, NOS2, IL-1B, CCL2, CD3G, FOS, CD3D, MYD88, MAPK13
KEGG_PATHWAY	hsa04114	Oocyte meiosis	11	0.017478	CDC20, CCNB2, CCNB1, PTTG1, CALML5, CCNE2, CCNE1, CDK1, CALML3, MAD2L1, AURKA
KEGG_PATHWAY	hsa00592	Alpha-Linolenic acid metabolism	5	0.018996	PLA2G2F, FADS2, PLA2G4D, PLA2G2A, PLA2G3
KEGG_PATHWAY	hsa05168	Herpes simplex infection	15	0.020979	DDX58, STAT1, TAP1, FOS, IFIT1, SOCS3, OAS1, OAS2, IL-1B, OAS3, IRF7, CDK1, CCL2, MYD88, IRF9
KEGG_PATHWAY	hsa04380	Osteoclast differentiation	12	0.021031	FOSL1, SOCS3, FCGR3B, STAT1, LCK, IL-1B, BLNK, ACP5, FOS, JUNB, IRF9, MAPK13
KEGG_PATHWAY	hsa04064	NF-kappa B signaling pathway	9	0.028614	LYN, BCL2A1, DDX58, LCK, IL-1B, BLNK, PRKCQ, CCL19, MYD88
KEGG_PATHWAY	hsa04621	NOD-like receptor signaling pathway	7	0.028679	PYCARD, IL-1B, CARD6, CCL2, CXCL1, NOD2, MAPK13
KEGG_PATHWAY	hsa00591	Linoleic acid metabolism	5	0.031316	PLA2G2F, PLA2G4D, PLA2G2A, PLA2G3, CYP2E1
KEGG_PATHWAY	hsa00120	Primary bile acid biosynthesis	4	0.031945	CYP39A1, CH25H, ACOX2, CYP7B1
KEGG_PATHWAY	hsa00140	Steroid hormone biosynthesis	7	0.033377	SULT2B1, HSD11B1, STS, HSD3B1, HSD17B2, CYP2E1, CYP7B1
KEGG_PATHWAY	hsa01100	Metabolic pathways	64	0.037857	ST6GALNAC1, GDA, GLDC, PIK3C2G, PYGL, HK2, SMPD3, IL4I1, HPGDS, PNP, ACADL, SPTLC2, KYNU, NAMPT, LIPG, HYAL4, PGM2, TK1, UPP1, AASS, PLA2G4D, ARG1, GPT2, AMPD3, NME1, ALDH3A1, PLCB4, ACOX2, CMPK2, ACSBG1, CYP2E1, IDO1, PLA2G3, ALOX12B, FUT2, CYP2C18, FUT1, FUT3, TYMP, HSD11B1, UGCG, RDH12, HSD17B2, RDH16, ATP6V0A4, XDH, HAO2, PLA2G2F, GALNT6, RRM2, GK, GCH1, NOS2, PLA2G2A, HSD3B1, CYP4F8, ALDH4A1, SQLE, HAL, AKR1B10, DHRS9, POLE2, POLR3G, HPSE
KEGG_PATHWAY	hsa05143	African trypanosomiasis	5	0.047416	PLCB4, IL-1B, SELE, MYD88, IDO1

Table 4 Kyoto Encyclopedia of Genes and Genomics function enrichment of target differentially expressed mRNAs

Category	hsa	Term	Count	P value	Genes
KEGG_PATHWAY	hsa05164	Influenza A	6	0.002804	STAT1, OAS2, IL-1B, OAS3, TNFSF10, MAPK13
KEGG_PATHWAY	hsa05160	Hepatitis C	5	0.006506	STAT1, OAS2, CLDN8, OAS3, MAPK13
KEGG_PATHWAY	hsa05162	Measles	5	0.006506	STAT1, OAS2, IL-1B, OAS3, TNFSF10
KEGG_PATHWAY	hsa04062	Chemokine signaling pathway	5	0.020355	CXCL9, CCL8, PLCB4, CCL22, STAT1
KEGG_PATHWAY	hsa04620	Toll-like receptor signaling pathway	4	0.021751	CXCL9, STAT1, IL-1B, MAPK13
KEGG_PATHWAY	hsa04060	Cytokine-cytokine receptor interaction	5	0.047526	CXCL9, CCL8, CCL22, IL-1B, TNFSF10

Table 5 Primer sequence in the real-time polymerase chain reaction

Primer name	Primer sequence, 5’ to 3’
GAPDH-F (internal reference)	5-GGAGCGAGATCCCTCCAAAAT-3
GAPDH-R (internal reference)	5-GGCTGTTGTCATACTTCTCATGG-3
ACTB-F (internal reference)	5-CATGTACGTTGCTATCCAGGC-3
ACTB-R (internal reference)	5-CTCCTTAATGTCACGCACGAT-3
IL-1B-F	5-TTCGACACATGGGATAACGAGG-3
IL-1B-R	5-TTTTTGCTGTGAGTCCCGGAG-3
CXCL9-F	5-CCAGTAGTGAGAAAGGGTCGC-3
CXCL9-R	5-AGGGCTTGGGGCAAATTGTT-3
CCL8-F	5-TGGAGAGCTACACAAGAATCACC-3
CCL8-R	5-TGGTCCAGATGCTTCATGGAA-3
CLDN8-F	5-CTACAGGCAGCCAGAGGACT-3
CLDN8-R	5-ACAGGGATGAGCACCACCAT-3
hsa-U6 (internal reference)
hsa-miR-30a-3p	5-CTTTCAGTCGGATGTTTGCAGC-3
hsa-miR-181a-5p	5-AACATTCAACGCTGTCGGTGAGT-3
hsa-miR-21-5p	5-TAGCTTATCAGACTGATGTTGA-3