The underlying molecular mechanism and identification of transcription factor markers for laryngeal squamous cell carcinoma

Figures & data

Figure 1. Flow chart of this study. LSCC: laryngeal squamous cell carcinoma; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; PPI: protein-protein interaction; DEGs: differential expression genes; TF: transcription factor; ChIP-Seq, chromatin immunoprecipitation sequencing

Figure 2. Screening processes for datasets included in the study

Table 1. Basic information of each dataset

Dataset	Database	Platform	n ^a of samples		n of DEGs ^b
			LSCC ^c	Non-LSCC	Up-DEGs ^d	Down-DEGs ^e
E-MEXP-44	ArrayExpress	A-AFFY-1/ A-AFFY-32	8	8	66	59
GSE29330	GEO ^f	GPL570	3	5	436	303
GSE51985	GEO	GPL10558	10	10	382	458
GSE58911	GEO	GPL6244	7	7	75	284
GSE59102	GEO	GPL6480	29	13	1493	1667
GSE84957	GEO	GPL17843	9	9	618	422
GSE107591	GEO	GPL6244	4	4	16	15
RNA-Seq	TCGA ^g	-	111	12	5557	2940

^a: number; ^b: differential expression genes; ^c: laryngeal squamous cell carcinoma; ^d:up-regulated differential expression genes; ^e:down-regulated differential expression genes; ^f:Gene Expression Omnibus; ^g:the Cancer Genome Atlas.

Figure 3. Volcano plots of differential expression genes in E-MEXP-44 (a), GSE29330 (b), GSE51985 (c), GSE58911 (d), GSE59102 (e), GSE84957 (f), GSE107591 (g) and TCGA (h). Up: up-regulated genes; Down: down-regulated genes

Figure 4. Gene Ontology (GO) analysis for identified up-regulated differential expression genes. Cellular components (a), biological processes (b) and molecular functions (c) of identified up-regulated differential expression genes. The blue nodes in the concentric circles represent genes clustered in specific GO terms. The larger size and darker color of the internal departments represent the more significant enrichment of GO term

Figure 5. Gene Ontology (GO) analysis for identified down-regulated differential expression genes. Cellular components (a), biological processes (b) and molecular functions (c) of identified down-regulated differential expression genes. The blue nodes in the concentric circles represent genes clustered in specific GO terms. The larger size and darker color of the internal departments represent the more significant enrichment of GO term

Figure 6. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of identified up-regulated differential expression genes (a) and identified down-regulated differential expression genes (b). Different color bands correspond to different KEGG enrichment pathways

Figure 7. Protein-protein interaction (PPI) analysis for identified up-regulated differential expression genes (a) and identified down-regulated differential expression genes (b)

Figure 8. Kaplan-Meier curves of transcription factors related to laryngeal squamous cell carcinoma prognosis. CHD4 (a); BCAT1 (b); FOXA2 (c); GATA6 (d); HNF1A (e); HOXB13 (f); MAFF (g); TCF4 (h)

Figure 9. Forest plots for identifying transcription factors independently related to LSCC prognosis. A: univariate Cox analysis; B: multivariate Cox analysis. N: number of samples; * p < 0.05; ** p < 0.005; *** p < 0.001

Figure 10. Expression of HOXB13 and its screening effect in laryngeal squamous cell carcinoma (LSCC). A: forest plot with standard mean difference (SMD) for evaluating deferential expression of HOXB13 between LSCC tissues and non-LSCC tissues. B: funnel plot with Egger’s test; C: summary receiver-operating curve

Data availability statement

All datasets used in the research can be found in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/, containing the dataset of E-MEXP-44), Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/, containing datasets of GSE29330, GSE51985, GSE58911, GSE59102, GSE84957, GSE107591), and the Genomic Data Download from Commons Data Portal (https://portal.gdc.cancer.gov/repository, containing an RNA-Seq dataset related to laryngeal squamous cell carcinoma) databases.