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.