Integrated bioinformatics analysis of miRNA expression in osteosarcoma

Figures & data

Figure 1. The analysis process of this study.

Table 1. Information of all seven data sets.

Data set	Samples	Assay type	Number of miRNA probes	Validated
1	Seven osteosarcoma tumor samples(OS4, OS7, OS9, OS11, OS15, OS17, OS18)	Agilent	799	qRT-PCR
2	19 osteosarcoma cell lines	Agilent	799	qRT-PR
3	OS versus control tissues	Agilent	1100	qRT-PR
4	osteosarcoma cell lines	LC Sciences	–	qRT-PR
5	Osteosarcoma cell line (MG – 63) and osteoblast cell line	Illumina	1146	qRT-PCR
6	23 patients with osteosarcoma, 3 normal muscle tissues	miRCURY LNA	–	qRT-PCR
7	OS versus control tissues	Illumina	1135	qRT-PCR

Figure 2. Distribution of DEMs alterations in OS as reported by primary studies. Short vertical bars indicate down- or up-regulated miRNA. There were significant differences in both up-regulated and down-regulated miRNAs between different data sets.

Figure 3. Statistics of the number of up- and down-regulated miRNA in the existing seven independent miRNA expression data set in osteosarcoma the left pillars in each dataset represents the quantity of up-regulated miRNA compared with the normal sample tissue expression; the right pillars in each dataset represents the quantity of down-regulated miRNA.

Figure 4. Number of up- and down-regulated miRNA correspond to the seven independent data set.

Table 2. List of miRNA with meta characteristics in osteosarcoma.

miRNA	chromosome	beg	end	strand	supporteddata sets
Upregulated
hsa-miR-106	chr7	100093993	100094074	−	3
hsa-miR-17	chr13	91350605	91350688	+	3
hsa-miR-181	chr19	13874699	13874808	+	8
hsa-miR-19	chr13	91350891	91350972	+	3
Downregulated
hsa-miR-126	chr9	136670602	136670686	+	4
hsa-miR-127	chr14	100882979	100883075	+	3
hsa-miR-133	chr18	21825698	21825785	−	4
hsa-miR-150	chr19	49500785	49500868	−	3
hsa-miR-335	chr7	130496111	130496204	+	4
hsa-miR-376	chr14	101040782	101040849	+	7
hsa-miR-409	chr14	101065300	101065378	+	3
hsa-miR-451	chr17	28861369	28861440	−	3

Figure 5. Metabolic pathways enrichment of target genes of miRNA Target genes of Seven out of 12 DEMs possessed appropriate Pathway enrichment. The gradient from green to red represents the corresponding Pathway proportion (%) of the terms in the miRNA target genes, and the deeper the color, the higher the proportion.

Table 3. GO annotation of target genes of up-regulated miRNA in osteosarcoma.

Category	Term	Count	%	P value	Foldenrichment	FDR	Fisher exact
GOTERM_BP_FAT	regulation of transcription	438	2.2	4.90E-25	1.5	9.00E-22	3.00E-25
GOTERM_BP_FAT	transcription	360	1.8	2.40E-21	1.6	4.50E-18	1.40E-21
GOTERM_BP_FAT	regulation of RNA metabolic process	318	1.6	3.10E-20	1.6	5.70E-17	1.80E-20
GOTERM_BP_FAT	regulation of transcription, DNA-dependent	312	1.6	4.70E-20	1.6	8.70E-17	2.70E-20
GOTERM_BP_FAT	regulation of transcription from RNA polymerase II promoter	141	0.7	5.50E-12	1.8	1.00E-08	2.70E-12
GOTERM_BP_FAT	homophilic cell adhesion	42	0.2	1.90E-10	2.9	3.40E-07	4.90E-11
GOTERM_BP_FAT	positive regulation of transcription, DNA-dependent	95	0.5	6.10E-09	1.8	1.10E-05	3.00E-09
GOTERM_BP_FAT	positive regulation of RNA metabolic process	95	0.5	9.50E-09	1.8	1.80E-05	4.70E-09
GOTERM_BP_FAT	positive regulation of gene expression	108	0.5	2.50E-08	1.7	4.60E-05	1.30E-08
GOTERM_BP_FAT	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	114	0.6	2.60E-08	1.7	4.80E-05	1.40E-08

Table 4. GO annotation of target genes of down-regulated miRNA in osteosarcoma.

Category	Term	Count	%	P value	Foldenrichment	FDR	Fisher exact
GOTERM_BP_FAT	regulation of phosphorus metabolic process	36	0.6	1.20E-04	2	2.10E-01	5.80E-05
GOTERM_BP_FAT	regulation of phosphate metabolic process	36	0.6	1.20E-04	2	2.10E-01	5.80E-05
GOTERM_BP_FAT	response to tumor necrosis factor	5	0.1	1.00E-03	10.4	1.80E + 00	6.90E-05
GOTERM_BP_FAT	positive regulation of cell proliferation	32	0.5	1.60E-04	2.1	2.70E-01	7.00E-05
GOTERM_BP_FAT	regulation of phosphorylation	34	0.5	2.70E-04	2	4.70E-01	1.30E-04
GOTERM_BP_FAT	regulation of kinase activity	28	0.5	3.50E-04	2.1	6.10E-01	1.50E-04
GOTERM_BP_FAT	regulation of protein kinase activity	27	0.4	4.70E-04	2.1	8.30E-01	2.10E-04
GOTERM_BP_FAT	regulation of transferase activity	28	0.5	6.60E-04	2	1.20E + 00	3.10E-04
GOTERM_BP_FAT	positive regulation of fatty acid beta-oxidation	3	0	1.30E-02	16.2	2.00E + 01	4.80E-04
GOTERM_BP_FAT	protein heterooligomerization	8	0.1	2.90E-03	4.2	4.90E + 00	6.00E-04

Figure 6. Metabolic pathways enrichment analysis of target genes of up-regulated miRNA in osteosarcoma Target genes of up-regulated miRNA were mainly enriched in four pathways, with cancer possessing the highest enrichment degree.

Figure 7. Transcription factor analysis of target genes of up- and down-regulated miRNAs. (A) Share and specific transcription factor comparison of target genes of up- and down-regulated miRNA. The left background represents number of transcription factors of target genes of up-regulated miRNA. The right background on behalf of number of transcription factors of target genes of down-regulated miRNA. (B) E-value and cross ratio statistics of important regulating transcription factors.