Gene expression and common DEGs
In this study, we analyzed the DEGs to find similar genes among three types of cells. Analysis showed that antibody-secreting Cells (AS), cardiac mesenchymal stromal cells (c-MSC), and skeletal muscle cells have 549, 509, and 1744 DEGs respectively the majority of them are up-regulated genes (Fig. 1a). 9 DEGs among all types are common and there are much more common DEGs between c-MSC and skeletal muscle cells in comparison with others. For this goal, the Venn diagram was used for showing overlap among genes (Fig. 1b). In addition, most of these DEGs have up-regulated genes except Hdc, Pilra (in ASCs), and Hspa1a (in cMSCs) (Fig. 1c).
Gene ontology
Gene Ontology analysis (GO) illustrates how genes are connected to a biological system, part of the body, or function. GO showed that change in some pathway such as regulation of transcription, cell cycle, immune system process, cell differentiation and so on which top 5 of all cells was determined by a bar chart (Fig. 2a). furthermore, common pathways among them were fund including immune system process, apoptotic process, aging, etc (Fig. 2b).
Protein-protein interaction network analysis
Protein-protein interaction (PPI) networks depict how genes encoded proteins interact with one another physically or functionally. Protein groups may be discovered using subnetworks, which can be found using network-based analysis. Using the information found in the STRING database, PPI networks were built for each kind of cell. Then, complex sub-networks and highly interconnected core proteins were found. We also discovered underlying biological processes utilizing the gene ontology of sub-networks. According to network analysis, the ASC network had 240 nodes and 593 edges. in addition, we found 5 sub-network that played role in nucleosome assembly, tRNA aminoacylation for protein translation, protein N-linked glycosylation via asparagine, protein folding, and mRNA splicing, via spliceosome (Fig. 3a). the c-MSC network had 92 nodes and 76 edges and also had one sub-network related to negative regulation of the apoptotic process (Fig. 3b). eventually, we found 436 nodes and 607 edges for the SMC network that had 8 sub-networks such as microtubule-based process, translation, RNA splicing, and so on (Fig. 3c). furthermore, by comparison of proteins, we found 2 proteins, Slpi and Hspa1a, which are common among them (Fig. 3d).
Transcription factor analysis
First, a gene regulatory network was built (Supplementary) by the use of TFs after that DE-TFs detect which include E2F1, MYB, GFI1B, and NUCKS1 for ASC all of them are up-regulated (Fig. 4a). c-MSC had just one up-regulated DE-TF, JARID2 (Fig. 4b). plus PRDM14, RUNX1, and TRP63 were detected as DE-TFs for SMC in a way that all of them were up-regulated (Fig. 4c). eventually, we fund 12 TF among three types of cells that are common for example SLPI, RUNX1, RNF2, etc (Fig. 4d).