Figure 1.
The expression profiles of LncRNAs and mRNAs in DN, DP, CD4+ and CD4+A T cells.
The DN, DP, CD4+ and CD4+A T cells and their total RNA were prepared as described, the expression of (a) LncRNAs and (b) mRNAs were detected on an Agilent microarray. The raw data are displayed in a heatmap.
Figure 2.
The expression profiles of two LncRNAs and four mRNAs in the T cell development and activation process.
(a) A heatmap of two LncRNAs and four mRNAs in the T cell development and activation process. (b–g) The expression patterns of two LncRNAs and four mRNAs in 4 cell lines as monitored by RT-qPCR. Unlike letters associated with bars on the histogram indicate a significant difference, (P<0.05).
Figure 3.
A log-log scatterplot comparing the global mRNA and LncRNA expression profiles between four subsets of CD4+ T cells.
(a,d) A log-log scatter plot between DN and DP, (b,e) a log-log scatter plot between DP and CD4+, and (c,f) a log-log scatter plot between CD4+ and CD4+A. Red dots indicate significant differences and the black dots indicate no significant differences.
Table 1.
The top 10 up- and down-regulated LncRNAs in the DN VS. DP group.
Table 2.
The top 10 up- and down-regulated LncRNAs in the DP VS. CD4+ group.
Table 3.
The top 10 up- and down-regulated LncRNAs in the CD4+ VS. CD4+A group.
Table 4.
The number of up- and down-regulated LncRNAs and mRNAs in the different comparison groups.
Figure 4.
A correlation heatmap between the differentially expressed LncRNAs and genes.
Rows represent differentially expressed genes, and the columns represent differentially expressed LncRNAs. A pink color indicates a positive correlation, while blue-green indicates a negative correlation. (a) DP VS. DN; (b) CD4+ VS. DP; and (c) CD4+A VS. CD4+.
Figure 5.
A topological graph displaying the regulation network between the LncRNAs and mRNAs.
(a) DP VS. DN; (b) CD4+ VS. DP; and (c) CD4+A VS. CD4+.
Figure 6.
Results of the GO analysis of the genes with sequences matching LncRNAs. –log10(P) indicates the GO score related to the genes with a biological process P value.
(a) T cell function related biological processes of the LncRNA sequence matched genes in the DP VS. DN group; (b) T cell function related biological processes of the LncRNA sequence matched genes in the CD4+ VS. DP group; (c) T cell function related biological processes of the LncRNA sequence matched genes in the CD4+A VS. CD4+ group.
Figure 7.
Results of the GO analysis of the genes neighboring LncRNA. –log10(P) indicates the GO score related to genes with a biological process P value.
(a) The main biological processes of the LncRNA neighboring genes in the DP VS. DN group; (b) the main biological processes of the LncRNA neighboring genes in the CD4+ VS. DP group; and (c) the main biological processes of the LncRNA neighboring genes in the CD4+A VS. CD4+ group.