Fig. legends:
Fig. 1. A) Principle Component Analysis (PCA) of the neural progenitor cells and their differentiated neurons on the 2D and 3D porous polystyrene. PCA shows the distribution of the samples. B and C) Gene set enrichment analysis of the most up regulated genes in the presence of 2D and 3D scaffold respectively. D) Venn diagram shows comparison between the number of differentially expressed genes between 2D and 3D scaffolds. E) Gene set enrichment analysis of the common differentially expressed genes between 2D and 3D scaffold. F) Heatmap plot indicating the common differentially expressed genes between 2D and 3D scaffold. Red color shows up regulated genes and green color indicates down regulated ones. G and H) Biological process analysis of the genes that exclusively up regulated in 2D and 3D scaffolds respectively.
Fig. 2. a) biological process analysis of the up regulated genes in the degradable PEGs. The terms are ordered according to their -log10 p-value. The number of genes in each term is represented in front of each term. b) Gene regulatory network for the inflammatory response related genes in the intestinal stem cells. Each gene is represented by a node and interaction between them is represented by edge. The red color shows up regulation of the genes and the green one shows down regulation of them. The intensity of the color shows the amount of the expression changes. c) Centrality analysis of the gene regulatory network. Transcription factors are represented in the x bar and the numbers of interactions are indicated in the y bar. D) Protein complexes which is obtained from protein-protein interaction network of the differentially expressed TFs.
Fig. 3. a) Venn diagram shows the total number of differentially expressed genes and those that exclusively expressed in osteoblast generated from different origins. b) gene ontology analysis of the common differentially expressed genes of MSCs-differentiated osteoblast which are generated from different origins. c and d) gene set enrichment analysis of the up regulated genes in the osteoblast generated from iPSC-MSCs and ESC-MSCs respectively. e) gene regulatory network for genes exclusively involved in the differentiation of ESC-MSCs into osteoblasts and mapped expression of ESC-MSCs generated osteoblast, f) iPCS-MSCs and g) BM-MSCs derived osteoblast on the regulatory network. h) Ontology analysis of the regulatory network. The cell cycle related terms are colored in red. Majority of the genes in these terms are down regulated.