Identification of species-specific expressed genes

     There are three steps for identifying species-specific expressed genes in the same cell type (e.g. cell type A) after performing single-cell clustering.

     First, identify cell types in two species using known marker genes.

     Second, in each species identify all marker genes (or differentially expressed genes) of cell type A relative to other cell types using Seurat software.

     Third, compare marker genes (or differentially expressed genes) of cell type A from two species. The genes are species-specific if they are present only in one species. If the genes are present in two species, perform statistical test to assess whether the genes are specific-specific expressed as following: (i) for each species get the rank of genes in expression level in cell type A; (ii) for each gene calculate the significance of Wilcoxon rank test according to the rank of the gene; (iii) determine whether the genes are specific-specific expressed accoring to the significance of Wilcoxon rank test.

     Please also refer to the part of materials and methods in the article 'Gene regulatory networks controlling vertebrate retinal regeneration': bulk RNA-seq data analysis, and identification of cell types and markers for each cluster.

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