Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis

Figures

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  Figure 1. Volcano plot and Hierarchical Clustering Map. Up-regulated (red dot) or down-regulated (green dot) lncRNAs (A) and mRNAs (B) were identified between obese and non-obese group in Volcano plot. (C) Hierarchical Clustering analysis of differentially expressed lncRNAs between obese and non-obese group; (D) Hierarchical Clustering analysis of differentially expressed mRNAs between obese and non-obese group. Vertical axis represents differentially expressed genes. Red color indicates high relative expression and green color indicates low relative expression. Horizontal axis represents the names of samples. OB represent the obese individual (obese group), NC represent the non-obese individual (control group).

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  Figure 2. GO and pathway analysis. Red, green and blue bars represent Biological Process, Cellular Component, and Molecular Function, respectively. (A) Top 10 significantly up-regulated GO terms for differentially expressed mRNAs. (B) Top 10 down-regulated GO terms for differentially expressed mRNAs. The terms were divided into three categories, including biological process (BP, red), cellular component (CC, green), and molecular function (MF, blue). (C) The significantly up-regulated GO terms of BP for differentially expressed mRNAs. (D) The significantly down-regulated GO terms of BP for differentially expressed mRNAs. (E) Top 10 significantly up-regulated pathways of differentially expressed mRNAs. (F) Top 10 significantly down-regulated pathways of differentially expressed mRNAs.

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  Figure 3. LncRNA-mRNA co-expression network. Blue and red nodes represent lncRNAs and mRNAs, respectively. Node size represents the degree. (A) 10 lncRNAs with higher core degrees and fold change interacted with 91 mRNAs. (B) 30 lncRNAs interacted with 10 mRNAs in the GO term of inflammatory response. (C) 43 lncRNAs interacted with 11 mRNAs in the GO term of lipid metabolic process.

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  Figure 4. Top 4 modules from the protein-protein interaction network indicated by STRING. Line thickness indicates the strength of data support. (A) Module 1, (B) The enriched KEGG pathways of module 1. (C) Module 2, (D) The enriched KEGG pathways of module 2. (E) Module 3, (F) The enriched KEGG pathways of module 3. (G) Module 4, (H) The enriched KEGG pathways of module 4.

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  Figure 5. Validation of Microarray Data by qRT-PCR. Three up-regulated and three down-regulated lncRNAs were validated by qRT-PCR in adipose tissues of obese (n = 31) and non-obese (n = 31) children. The heights of the columns represent the mean expression value of log transformed fold changes (obese/non-obese).

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  Figure 6. Knockdown RP11-20G13.3 in SW872 cells reduced adipogenesis. (A) lncRNA RP11-20G13.3 expression in the differentiation progress of SW872 preadipocytes at 0 h, 24 h, 48 h and 72 h. (B) Knockdown efficiencies of three kinds of siRNA targeting to RP11-20G13.3 were validated by qRT-PCR. (C) Oil Red O staining analysis in SW872 control and RP11-20G13.3-knockdown cells at 0 h, 48 h and 72 h. (D) The mRNA expression of PPARγ, C/EBPα and adiponectin during adipogenesis of control and RP11-20G13.3-knockdown cells at 0 h, 24 h, 48 h and 72 h. *P < 0.05, **P < 0.01 vs. control.