Self-organizing map of gene regulatory networks for cell phenotypes during reprogramming

The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflect the status of gene regulatory network in those reprogramming cells. In this study, we applied self-organizing maps (SOMs) on those complex gene expression data from different pluripotent cells, including partially reprogrammed and fully reprogrammed induced pluripotent cells (iPSCs), embryonic stem cells (ESCs), and adult stem cells came from different tissues. We showed that our SOMs have good correlation with the previously reported PluriNet of stem cells and they are pictorial diagrams which can reflect the intrinsic status of cells.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► We applied SOMs on complex gene expression data from different cells. ► SOMs can reflect the different expression patterns of reprogramming cells. ► SOMs are pictorial diagrams which can reflect the intrinsic status of cells.