Systematic analysis of co-expression network and gene expression profile of differentially expressed lncRNA-mRNA one week after spinal cord injury

Figures & data

Figure 1. Identified differential mRNA and lncRNA. A,B. Principal component analysis (PCA) of mRNA and lncRNA expression profiles. C,D. Volcano plot of DE mRNA and lncRNA. In the volcano plot, the X axis indicates the fold change, which is shown on a log₂ scale, and the Y axis indicates the P value, which is shown on a −log₁₀ scale. Red represents mRNA up-regulation and blue represents mRNA down-regulation. For mRNA, | log₂FC |>1 was selected, P < 0.05; for lncRNA, | log₂FC |>0.5 and P < 0.05 were selected, which were considered statistically different. E,F. RT-PCR to verify the top five lncRNAs with the most significant up-regulation and down-regulation trends. G. Heat map of DE mRNA and lncRNA. In the heat map, red indicates lncRNAs or mRNAs that were up-regulated, and blue indicates lncRNAs or mRNAs that were down-regulated.

Table 1. The top 10 up-regulated and down-regulated lncRNAs.

Up-regulated			Down-regulated
lncRNA	P value	log2(fold change)	lncRNA	P value	log2(fold change)
March1	1.35E-05	2.743295296	4930426D05Rik	0.000458608	−2.607306044
Dnm3os	0.002282278	2.180853923	Mirg	0.000433324	−2.412371428
Chmp4b	0.000222002	1.52105678	Ddc	1.22E-05	−2.208050112
Bend5	0.000137061	1.451610298	6720427I07Rik	0.001648962	−1.678405103
Wnk1	4.84E-05	1.403836495	Meg3	3.87E-05	−1.640526887
Gm26940	0.000302481	1.387629872	Shank1	2.63E-05	−1.513361431
Ski	0.000160067	0.95651036	Gm27028	0.002251338	−1.452638715
Tlk1	7.83E-05	0.694536169	Fam196a	0.00201839	−1.424264429
Gm26691	0.00095133	0.685618598	Mfsd2a	0.000432778	−1.220212534
Zfand6	0.000522904	0.617593732	Gm12843	9.21E-05	−1.205030073

Figure 2. Functional enrichment analysis of differential mRNA after SCI. A,B. GO enrichment analysis and KEGG pathway enrichment analysis were performed for up-regulated mRNA. C,D. GO enrichment analysis and KEGG pathway enrichment analysis were performed for down-regulated mRNA. E. GSEA analysis of all mRNA expression profiles after SCI revealed the biological process. F. GSEA analysis of all mRNA expression profiles for KEGG pathway after SCI.

Figure 3. Construction of PPI network and GSEA analysis of hub gene and module gene function. A. Protein-protein interaction networks of DE mRNAs. Nodes indicate mRNAs. Lines represent the interactions between DE mRNAs. Changes in DE mRNA expression level were indicated by color changes, with red indicating up-regulation and blue indicating down-regulation. The 15 hub genes obtained by Degree algorithm in Cytohubba plug-in are represented by yellow border. B. Cluster calculation through Mcode plug-in, and the first four core sub-networks with scores greater than 4 are obtained. Top left: Cluster1, Score 7.7; Top right: Cluster2, Score 4.25; Bottom left: Cluster3, Score 4; Bottom right: Cluster4, Score 4. C. Biological processes involving hub genes in GSEA analysis. D. The biological processes involved in GSEA analysis of mRNA in corresponding Cluster.

Table 2. The hub genes and their corresponding degrees.

Gene	Degree	Gene	Degree	Gene	Degree	Gene	Degree
Stat3	27	Fn1	21	Shank1	16	Snap91	15
Snap25	26	Ngf	21	Camk2g	16	Ntrk3	14
Camk2a	25	Vegfa	20	Stxbp1	16	Nrxn1	14
Dlg2	23	Isl1	19	Bsn	16	Stx1b	13
Rbfox3	23	Erbb4	17	Cacng2	15	Syn2	13

Figure 4. Construction and functional analysis of lncRNA and mRNA co-expression network. A. Pearson correlation coefficient and P value of lncRNA and mRNA were calculated to obtain the correlation between co-expressed lncRNA and mRNA. Displayed by correlation heat map. B. The lncRNA-mRNA co-expression network was established by Cluego, and the biological process and pathway of mRNA were analyzed. C. The proportion of genes enriched by each biological process pathway is displayed by pie chart. D. The first 15 GO enrichment items obtained from the biological process pathway analysis of mRNA in the co-expression network were displayed.

Data availability statement

The data supporting the findings of this study are available in the figshare repository at https://doi.org/10.6084/m9.figshare.20065661.v3.