Analysis of the different characteristics between omental preadipocytes and differentiated white adipocytes using bioinformatics methods

Figures & data

Figure 1. Heatmap of 328 DEGs screened by limma package in R software. Red areas represent upregulated genes and green areas represent downregulated genes in the DIF and UNDIF group. DEG: differentially expressed gene; DIF: differentiated white adipocyte; UNDIF: undifferentiated preadipocytes.

Figure 2. Volcano plot analysis identifies DEGs. Red dots represent 185 upregulated genes and green dots represent 143 downregulated genes from the DIF and UNDIF group.

Table 1. Top 10 genes with the most neighbours and expanded nodes in Cytoscape

Gene symbol	Description	logFC
ASPM	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	−5.09168
DLGAP5	discs, large (Drosophila) homolog-associated protein 5	−3.55184
CCNB1	cyclin B1	−3.19147
NUSAP1	nucleolar and spindle associated protein 1	−2.94063
CCNB2	cyclin B2	−2.73109
CDK1	cyclin-dependent kinase 1	−2.56781
AURKB	aurora kinase B	−2.55832
TPX2	TPX2, microtubule-associated	−2.42251
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	−1.89074
BUB1	BUB1 mitotic checkpoint serine/threonine kinase	−1.55189

Figure 3. The PPI network of DGEs and the most significant modules of DEGs. (a) The PPI network was analysed by String software. There were 325 nodes and 655 edged in the PPI network. Red represents upregulated genes; green represents downregulated genes. (b) The most significant module identified by MCODE (score = 27.863) Dark blue represents the top 10 genes with the most neighbours and expanded nodes. DEG: differentially expressed gene; PPI: protein–protein interaction.

Figure 4. GO enrichment result of upregulated and downregulated DEGs respectively. Abscissa represents -LOG (pValue), and ordinate represents BP, CC, and MF terms. GO: Gene Ontology. BP: biological processes, CC: cellular components, MF molecular functions (MF).

Figure 5. KEGG enrichment result of upregulated and downregulated DEGs respectively. DEGs. Abscissa represents -Log (pValue), and ordinate represents KEGG terms. KEGG: Kyoto Encyclopedia of Genes and Genomes.

Table 2. Gene sets enrichment in GSEA analysis on GOBP and KEGG

Type of GSEA	Correlated with the differentiated white adipocytes	Enrichment of phenotype	Symbols
GOBP	Positively	Integrated stress response signalling	ASNS, ATF3, DDIT3, ATF4, PPP1R15A, HERPUD1
	Positively	Intrinsic apoptotic signalling pathway in response to endoplasmic reticulum stress	TRIB3, CHAC1, DDIT3, ATF4, PDX1, ITPR1, PPP1R15A, MAP3K5, HERPUD1
	Positively	Response to hyperoxia	PDGFRB, CDKN1A, FOXO1, BNIP3, PPARG
	Negatively	Positive regulation of transforming growth factor β production	MYB, SERPINF2, SMAD3, GATA6, FERMT1, CD200, PTGS2
	Negatively	Establishment of mitotic spindle orientation	NDE1, MAD2L1, GPSM2, CENPA, SPDL1, PLK, NDC80
	Negatively	Regulation of lymphocyte chemotaxis	CCL5, PTK2B, ADAM10, CCL2, CXCL14
KEGG	Positively	Glycolysis gluconeogenesis	PCK2, ALDH1B1, ADH1B, ALDOC, ADH1C, ENO2, ADH5, ADH1A, ALDH3A1, HK2, ADH7, PCK1, BPGM, LDHAL6B, ALDOB, ENO3, ALDH2, GPI FBP2, PGK2
	Positively	Histidine metabolism	MAOA, ALDH1B1, ALDH3A1, HNMT
	Positively	Glycine serine and threonine metabolis	PSAT1, MAOA, PHGDH, CBS, AOC3, PSPH, SHMT2, PIPOX, AGXT
	Negatively	Spliceosome	RBM25, DDX46, TRA2A, THOC1, SART1, LSM3, SF3B1, SRSF6, PUF60, THOC2, TXNL4A, SRSF10, SF3B2, SNRPE, PRPF31, TCERG1, SF3B3, PRPF19, SNRPC, PRPF40A, PPIE, SNRPB2, LSM2, DHX8, HNRNPA1, SNRPD1, SRSF3, SNRNP70, U2AF2, DDX23, SNRPD2, SF3B5, TRA2B, LSM6, NCBP1, SRSF7, SNRPA1, PRPF4, SNRPG, DHX15, LSM4, SRSF1, SNRPB, SNRPD3, SNRPF, HNRNPC, LSM7, HNRNPM, SNRPA, PPIH
	Negatively	Parkinson’s disease	PARK7, SDHC, COX4I1, COX6A1, NDUFV2, NDUFB4, COX7A2, NDUFS3, COX7B, COX7C, UBB, UQCRC2, NDUFA10, VDAC1, COX5B, APAF1, NDUFA6, SLC18A2, UBE2J1, COX5A, NDUFB7, UQCRQ, NDUFV, SNCAIP, NDUFA3, COX6B1, UQCR, SDHB, NDUFAB1, NDUFB8, CYC1, NDUFB2, NDUFB1, NDUFS7, SDHA, UBA1, HTRA2, NDUFA1, NDUFA2, NDUFB6, SLC25A5, NDUFS2, NDUFC1, NDUFS1, COX8A, NDUFA7
	Negatively	Proteasome	PSMD11, PSMC5, PSMD6, PSMB4, PSMD8, PSMB9, PSMB7, PSME3, PSMA4, PSMB10, PSMB6, PSMD4, PSMB5, PSMB3, PSMA2, PSMD3, PSMA5, PSMB8, PSMA7, PSMC3, PSMD13, PSMD2, PSME4

Figure 6. Gene sets enrichment in GSEA analysis of all altered genes on GOBP, KEGG. a: BP of GO analysis of all altered genes in GSEA. b: KEGG analysis of all altered genes in GSEA.

Data availability statement

The datasets generated for this study are available on request to the corresponding author.