Identification of potential micro-messenger RNAs (miRNA–mRNA) interaction network of osteosarcoma

Figures & data

Figure 1. (a) Volcano plots of DE-miRNAs. (b) Heatmap of DE-miRNAs

Figure 2. (a) Volcano plots of DE-mRNAs. (b) Heatmap of DE-mRNAs

Table 1A. The table shows the information of Top 20 differentially expressed miRNAs

ID	logFC	adj.P.Val	Regulated
hsa-miR-671-5p	4.546784	1.29E-23	up
hsa-miR-375	4.310829	1.81E-13	up
hsa-miR-490-3p	4.253599	2.50E-16	up
hsa-miR-203a	4.17923	1.29E-17	up
hsa-miR-150-5p	3.876575	1.32E-14	up
hsa-miR-499a-5p	3.780643	5.35E-23	up
hsa-miR-663a	3.706472	2.24E-22	up
hsa-miR-744-5p	−3.6605 C9	1.29E-26	down
hsa-miR-127-3p	−3.59745	4.82E-18	down
hsa-miR-31-5p	3.558546	1.98E-18	up
hsa-miR-331-3p	−3.55621	5.35E-23	down
hsa-miR-206	3.360764	4.28E-13	up
hsa-miR-144-5p	3.312609	1.06E-14	up
hsa-miR-10b-5p	3.305259	5.98E-10	up
hsa-miR-624-5p	3.2403	1.18E-27	up
hsa-miR-181d	3.186622	1.56E-19	up
hsa-miR-503-5p	−3.16267	6.39E-17	down
hsa-miR-502-5p	3.080622	3.82E-18	up
hsa-miR-95	2.981734	4.65E-23	up
hsa-miR-337-3p	−2.96696	8.44E-19	down

Table 1B. The table shows the information of Top 20 differentially expressed mRNAs

ID	logFC	adj.P.Val	Regulated
SPP1	6.949825862	1.64E-09	up
SEPP1	6.923031057	2.41E-12	up
MAFB	5.90485027	5.97E-11	up
LUM	5.900095106	1.84E-06	up
CTSK	5.850469544	8.03E-06	up
A2M	5.45878503	4.63E-07	up
COL1A2	5.379133987	2.35E-05	up
OLFML2B	5.320771951	2.49E-08	up
IBSP	5.302998023	0.002672362	up
ENPP2	5.265582743	9.05E-06	up
HLA-DRA	5.040214057	2.79E-06	up
MMP9	4.989747551	0.000505257	up
HBB	4.891442564	0.000388009	up
MGP	4.868326448	0.000297807	up
LYZ	4.836968258	5.28E-05	up
COL15A1	4.548971176	3.93E-06	up
MXRA5	4.474484032	4.27E-05	up
KRT18	−4.363851615	4.35E-06	down
DCN	4.299072964	0.000630991	up
LRRC15	4.253669709	5.95E-06	up

Figure 3. (a) Top 10 TF of up-regulated DE-miRNAs. (b) Top 10 TF of down-regulated DE-miRNAs

Figure 3. Continued

Table 2. The table shows the information of intersection genes

mRNA	Genes name
Upregulated	MMP2, COL1A1, TMEM59, OPN3, CDH11, DAAM2, PABPN1, VCAN, SULF1, MYO1D, TWIST1, COL1A2, SAT1, MEF2C, PTN, GPR137B, YTHDF3, SATB2, TMEM47, OXR1, DDIT4, FOS, PTBP2, DDR2, COL5A1, GHR, EVI2A, NDNF, PRRX1, SPP1, CTSK, CSGALNACT1, NID2, COL16A1, MAFB, P4HA1, COL4A1, ATP10D, PLEKHA5, SATB1, VAMP8, GJA1, BTG1, COL15A1, LRRC17, MARCKS, FAP, FAM46A, CSAD, DLX5, ZEB2, OLFML2B, LPAR6, LRP4, SNAI2
Downregulated	ITGA3, GCLM, SNAPC1, PPID, OIP5, KIF23, TUBB2B, PAX6, ODC1, FZD2, CTGF, ZNF580, TFDP1, DRAP1, FOSL1, TLN1, S100A2, TPM2, FHL2, KHDRBS3, HMGA1

Figure 4. (a) Venn diagram of common differentially expressed genes from the two datasets. DE-mRNAs were down-regulated in the dataset. (b) Venn diagram of common differentially expressed genes from the two datasets. DE-mRNAs were up-regulated in the dataset

Figure 5. (a) GO functional annotation of 76 dysregulated mRNAs. Top 10 GO terms of 76 dysregulated mRNAs in three categories (CC, BP, MF). (b) GO functional annotation of 76 dysregulated mRNAs. Top GO terms and their enriched mRNAs. (c) KEGG pathway enrichment analysis of 76 dysregulated mRNAs. Top 10 KEGG enrichment pathways of 76 dysregulated mRNAs. (d) KEGG pathway enrichment analysis of 76 dysregulated mRNAs. Top 10 KEGG enrichment pathways and their enriched mRNAs

Figure 5. Continued

Figure 5. Continued

Figure 5. Continued

Figure 6. (a) GO functional annotation of 55 up-regulated mRNAs. Top 10 GO terms of 55 up-regulated mRNAs in three categories (CC, BP, MF). (b) GO functional annotation of 55 up-regulated mRNAs. Top GO terms and their enriched mRNAs. (c) KEGG pathway enrichment analysis of 55 up-regulated. Top 10 KEGG enrichment pathways of 55 up-regulated mRNAs. (d) KEGG pathway enrichment analysis of 55 up-regulated mRNAs. Top 10 KEGG enrichment pathways and their enriched mRNAs

Figure 6. Continued

Figure 6. Continued

Figure 6. Continued

Figure 7. (a) GO functional annotation of 21 down-regulated mRNAs. Top 10 GO terms of 21 down-regulated mRNAs in three categories (CC, BP, MF). (b) GO functional annotation of 21 down-regulated mRNAs. Top GO terms and their enriched mRNAs

Figure 8. (a) The miRNA–mRNA networks of all dysregulated mRNAs. (b) The miRNA–mRNA networks of up-regulated mRNAs. (c) The miRNA–mRNA networks of down-regulated mRNAs

Figure 9. (a) PPI network of all dysregulated mRNAs. (b) PPI network of up-regulated mRNAs. (c) PPI network of down-regulated mRNAs

Table 3. The table shows the information of hub miRNAs

miRNA	Type	mRNA
hsa-miR-30d-5p	Down	CSAD, DDIT4, FAM46A, FAP, GJA1, LRRC17, OXR1, P4HA1
hsa-miR-17-5p	Down	CSGALNACT1, GJA1, GPR137B, MMP2, MYO1D, OXR1
hsa-miR-98-5p	Down	COL15A1,COL1A1, COL1A2, COL4A1, GHR, NID2, PRRX1
hsa-miR-301a-3p	Down	BTG1, GJA1, MAFB, SATB1, SATB2
hsa-miR-30e-5p	Down	CSAD, DDIT4, FAM46A, FAP, GJA1, LRRC17, OXR1, P4HA1, PRRX1
hsa-miR-181 c-5p	Down	COL16A1, DDIT4, EVI2A, PTBP2, SNAI2, SPP1

Table 4. The table shows the information of hub mRNAs, the information of hub mRNAs

mRNAs	Type	Degree	mRNAs	Type	Degree
COL1A1	Up	23	GJA1	Up	10
COL1A2	Up	20	SNAI2	Up	10
MMP2	Up	17	P4HA1	Up	8
CDH11	Up	13	VCAN	Up	8
COL4A1	Up	13	MEF2C	Up	7
COL5A1	Up	13	NID2	Up	7
CTGF	Down	12	ZEB2	Up	7
SPP1	Up	12	COL15A1	Up	6
TWIST1	Up	11	COL16A1	Up	6
FOS	Up	10	DDR2	Up	6