Identification of key gene pathways and coexpression networks of islets in human type 2 diabetes

Figures & data

Figure 1 A heat map of the top 10 upregulated DEGs and top 10 downregulated DEGs in 57 non-T2D islet samples and 20 T2D islet samples.

Notes: Red: upregulation; green: downregulation.
Abbreviations: DEGs, differentially expressed genes; T2D, type 2 diabetes.

Figure 2 Enrichment analyses for (A) GO terms (referred to as pathways) and (B) KEGG pathways of DEGs in T2D.

Notes: Blue: top 10 enriched pathways of upregulated DEGs. Black: top 10 enriched pathways of downregulated DEGs.
Abbreviations: DEGs, differentially expressed genes; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; T2D, type 2 diabetes.

Figure 3 A PPI network for T2D based on 957 DEGs constructed by Cytoscape.

Notes: Red indicates the upregulated DEGs. Blue indicates the downregulated DEGs.
Abbreviations: DEGs, differentially expressed genes; PPI, protein–protein interaction; T2D, type 2 diabetes.

Figure 4 Top three modules identified from the PPI network by Cytoscape (A, C, and E) and gene annotation enrichment analysis of biological process GO category for each module (B, D, and F).

Abbreviations: GO, Gene Ontology; PPI, protein–protein interaction.

Figure 5 Sample clustering and module detection.

Notes: (A) Sample dendrogram and trait indicator. The red color represents female and T2D samples, and the gray color represents no data in HbA1c. The color intensity was proportional to older age, higher BMI, and HbA1c levels. (B) Genes were clustered based on 1-TOM. Each colored branch indicates a module of highly connected genes. (C) The TOM plot shows the modules of gene expression by WGCNA.
Abbreviations: T2D, type 2 diabetes; TOM, topological overlap matrix; WGCNA, weighted correlation network analysis.

Figure 6 Correlation between modules and T2D.

Notes: (A) Heatmap of the module–trait relationships. P-values between the detected modules on the y-axis and clinical traits on the x-axis are shown in the box. Color indicates the direction of association (red means positive correlation; green means negative correlation). Hierarchical clustering dendrograms and heatmap of the trait T2D (B) or trait HbA1c (C). Each row and column in the heatmap corresponds to one module (labeled by color) or the trait (labeled by T2D or HbA1c). Red represents positive correlation, and blue represents negative correlation.
Abbreviation: T2D, type 2 diabetes.

Figure 7 Gene annotation enrichment analysis of KEGG pathway in each module.

Notes: (A) Magenta, (B) yellow, (C) turquoise, and (D) purple.
Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure S1 GO analysis classified the DEGs ([A] upregulated DEGs and [B] downregulated DEGs) into cellular component and molecular function of T2D. Abbreviations: DEG, differentially expressed genes; GO, Gene Ontology; T2D, type 2 diabetes.