Figure 1.
Changes in the expression of significantly deregulated miRNAs and mRNAs after each manipulation.
(A) Two-way hierarchical clustering of deregulated miRNAs resulting from all the six experimental manipulations, which are globally sorted into two groups, based on log2 fold changes. (B) One-way hierarchical clustering of deregulated mRNAs resulting from each manipulation based on log2 fold changes. Up- and downregulation of gene expression are represented by red and green colors, respectively, while black indicates no change relative to baseline levels. The number of (C) miRNAs and (D) mRNAs significantly deregulated by each manipulation, with the fraction of these that share targets with the manipulated molecule marked with red.
Figure 2.
The function of mRNAs with altered expression and their relationship to deregulated miRNAs after each manipulation.
The proportion of differentially expressed mRNAs in each type of relationship to deregulated miRNAs is shown in a pie chart, in which the intensity of the red color indicates the degree of association, with a more intense color representing a direct association; blue is used to indicate an unspecified relationship. The five biological processes most significantly enriched by altered mRNAs resulting from each manipulation are listed.
Figure 3.
Global views of functional miRNA-pathway regulation networks (MPRNs).
(A) Functional MRPNs resulting from each experimental manipulation. Green circles and blue triangles represent functional miRNAs and targeted pathways, respectively. The number and proportion of (B) miRNAs related to glioma and (C) pathways related to glioma in each MRPN, and (D) the overall proportion of miRNAs and pathways related to glioma in each MPRN are shown.
Figure 4.
Functional synergy and crosstalk between MPRNs activated by different targeted manipulations.
(A) Functional synergy and crosstalk between MPRNs activated by three miRNA targeted manipulations. Since miR-181d was upregulated by all the three manipulations, its target pathways and fold changes are provided. Green circles and blue triangles represent functional miRNAs and targeted pathways, respectively. (B) Functional synergy and crosstalk between MPRNs activated by three TF targeted manipulations. Since eight miRNAs were shared by all the three manipulations, their fold changes under all three manipulations are shown. (C) Example of functional synergy between MPRNs associated with manipulations targeting miRNAs and TFs. Since protein processing in the endoplasmic reticulum pathway was shared by +miR-181d, −miR-23b, −β-catenin, and −STAT3, miRNAs regulating this pathway are shown. The distribution of mRNAs with altered expression in this pathway is shown in the diagram, where purple, cyan, and red rectangles represent mRNAs deregulated by manipulations targeting miRNA, TFs, or both, respectively. HSP90B1 (circled in green) was downregulated by all the four experimental conditions.
Figure 5.
The comprehensive MPRN (cMPRN) and correlation between response frequency of miRNA-pathway regulations and their network centrality.
(A) cMPRN was generated by integrating the six MPRNs corresponding to each experimental manipulation. Green circles and blue triangles represent functional miRNAs and target pathways, respectively. Node size and edge thickness are correlated with response frequency. (B) The degree distribution of cMPRN follows the power law. (C) The degree of nodes (including pathways and miRNAs) was positively correlated with their response frequency to different manipulations. (D) The betweenness of edges (miRNA-pathway regulation) was positively correlated with their response frequency.
Figure 6.
Association between the core module of cMPRN and glioma patient survival.
(A) Green circles and blue triangles represent functional miRNAs and target pathways, respectively, in the core module. (B) Distribution of genes differentially expressed in the same direction under the three conditions sharing pathways in cancer: −STAT3, −β-catenin, and –miR-23b. Red and green rectangles represented genes that are up- and downregulated by the three experimental manipulations, while the white ones represent other genes within pathways in cancer. Red and green lines represent signal transduction downstream of these up- and downregulated genes, respectively. (C) Kaplan-Meier survival plot of the two subgroups of glioblastoma patients sorted by k-means clustering based on expression levels of either miRNA or mRNA signatures or both in the core module.