Cytoskeleton protein-protein interaction network during differentiation of human iPSCs to immature astrocyte

Cytoskeleton dramatically undergoes alterations during differentiation of human iPSCs (hiPSCs) to immature astrocyte.Protein complexes involved in changes in cytoskeleton structure remain unknown. The purpose of our study identify such protein complexes during differentiation of hiPSCs to immature astrocyte. We construct protein-protein interaction network based predicted protein-protein interactions to find these complexes.Method: Microarray data downloaded from GEO server using GSE43382 accession number. RMA and fold change algorithms wereused for normalization of raw data and detect differentially expressed (DE) genes respectively. DE genes submitted to DAVID for functional clustering. Clusters with enrichment score more than 1.3 assumed as meaningful clusters. Predicted protein-protein interactions retrieved from STRING database. Graph construction and visualization conducted usingcytoscape. Protein complexes identified using MCODE plugin of cytoscpe.Result: Comparison of immature astrocyte and hiPSCs show 2636 DE genes. List of DE genes accommodate 1413 up regulated DEgenes and 1223 down regulate genes. Cytoskeleton binding protein identified as most affected term based on p value in functional clustering analysis. This term contain 115 DE genes were used to find protein-protein interactions. Constructed network contain 145 nodes with 468 interactions. Analysis of protein-protein interaction result in identify protein complexwith 17 DE genes and 55 interactions. This complex assign 3.235 score to itself in our constructed network.Conclusion: This study for first time show most important protein complexes during hiPSCs differentiation to immature astrocyte that affects cytoskeleton structure and broaden our knowledge in differentiation process.

کلیدواژه ها:

Protein interaction network ، Protein complex ، hiPSC ، Astrocyte