Identification of key genes and molecular mechanisms associated with dedifferentiated liposarcoma based on bioinformatic methods

Figures & data

Figure 1 RNA degradation plots for all samples.

Notes: Our plotting result showed good parallel degradation curves of all samples (46 DDLPS; nine normal fat controls); no outstanding curve was observed. RNA degradation within all samples in this study was moderate and comparative. DD=DDLPS; FAT=normal fat control.
Abbreviation: DDLPS, dedifferentiated liposarcoma.

Figure 2 Differential gene expression pattern between DDLPS and the normal fat control.

Notes: (A) PCA for all included samples (DD = DDLPS; FAT= normal fat control). (B) Hierarchical clustering plot of gene expression for all samples. (C) Heat map for the identified DEGs.
Abbreviations: DDLPS, dedifferentiated liposarcoma; PCA, principal component analysis; DEGs, differentially expressed genes.

Table 1 Enriched GO terms and KEGG pathways for the identified DEGs

Category	Term	P-value	FDR
GOTERM_BP_FAT	GO:0010033:response to organic substance	2.85E–15	5.21E–12
GOTERM_BP_FAT	GO:0055114:oxidation–reduction	1.35E–13	2.43E–10
GOTERM_BP_FAT	GO:0009719:response to endogenous stimulus	1.53E–13	2.77E–10
GOTERM_BP_FAT	GO:0009725:response to hormone stimulus	1.65E–13	2.97E–10
GOTERM_BP_FAT	GO:0006006:glucose metabolic process	1.31E–12	2.36E–09
GOTERM_MF_FAT	GO:0031406:carboxylic acid binding	7.58E–12	1.18E–08
GOTERM_BP_FAT	GO:0019318:hexose metabolic process	2.24E–11	4.04E–08
GOTERM_BP_FAT	GO:0048545:response to steroid hormone stimulus	2.24E–11	4.04E–08
GOTERM_BP_FAT	GO:0042127:regulation of cell proliferation	1.24E–10	2.24E–07
GOTERM_BP_FAT	GO:0005996:monosaccharide metabolic process
KEGG_PATHWAY	hsa03320:PPAR signaling pathway	5.98E–06	0.00717
KEGG_PATHWAY	hsa00620:pyruvate metabolism	9.91E–06	0.011873
KEGG_PATHWAY	hsa04110:cell cycle	2.43E–05	0.029161

Abbreviations: GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEGs, differentially expressed genes; FDR, false discovery rate.

Figure 3 PPI network for DEGs.

Notes: In the network, the color of each node indicates the fold change in gene expression for each gene. In the color scale, dark red indicates up-regulation of gene expression, while green indicates down-regulation of gene expression. The magnitude of the circle of each node indicates the degree to which each gene is connected. Larger circles indicate a greater number of connections between the protein coded by the gene and other proteins. Ten filtered hub genes were labeled.
Abbreviations: PPI, protein–protein interaction; DEGs, differentially expressed genes.

Table 2 Identified hub genes in the PPI network

Gene	Degree
APP	96
MDM2	50
CDK1	24
PCNA	20
TKT	17
CDK4	17
CDC20	14
BUB1B	13
BARD1	13
ADRB2	13
LGALS3	12
CAV1	12
CCNA2	11
CDKN2A	10

Abbreviation: PPI, protein–protein interaction.

Figure S1 The actin and GAPDH 3′/5′ ratio tests for all samples (46 DDLPS; nine normal fat controls).

Note: These results confirmed that all the actin and GAPDH 3′/5′ ratios of included microarray raw profiles were <3 and that no bioB alert was found. DD=DDLPS; FAT=normal fat control.

Abbreviations: DDLPS, dedifferentiated liposarcoma; QC, quality control.

Figure S2 Maps of the three identified KEGG pathways.

Notes: (A) PPAR signaling pathway; (B) pyruvate metabolism pathway; and (C) cell cycle pathway. In the maps, red chips represent up-regulated DEGs, while green chips represent down-regulated DEGs. Copyright © Kanehisa Laboratories. Reproduced with permission.¹

Abbreviations: KEGG, Kyoto Encyclopedia of Genes and Genomes; DEGs, differentially expressed genes.

KanehisaMFurumichiMTanabeMSatoYMorishimaKNucleic Acids Res201745D135336127899587

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