CellSim: a novel software to calculate cell similarity and identify their co-regulation networks.

ABSTRACT

BACKGROUND: Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regulatory network. The position and function of cells in vivo, can provide some hints about the cell similarity. However, it still needs further clarification based on molecular level studies. RESULT: CellSim is therefore developed to offer a solution for cell similarity calculation and a tool of bioinformatics for researchers. CellSim is a novel tool for the similarity calculation of different cells based on cell ontology and molecular networks in over 2000 different human cell types and presents sharing regulation networks of part cells. CellSim can also calculate cell types by entering a list of genes, including more than 250 human normal tissue specific cell types and 130 cancer cell types. The results are shown in both tables and spider charts which can be preserved easily and freely. CONCLUSION: CellSim aims to provide a computational strategy for cell similarity and the identification of distinct cell types. Stable CellSim releases (Windows, Linux, and Mac OS/X) are available at www.cellsim.nwsuaflmz.com , and source code is available at https//github.com/lileijie1992/CellSim/ .