The present disclosure provides comprehensive and comparative flow cytometry-based methods for identifying the state of a biological system by identifying the phenotype of cells and correlating the phenotype with the gene expression profile of the cells, which is indicative of cell function. The cells can be immune cells from a subject suffering from immune -mediated disorders that result in imbalance of the immune system and impair a subject's ability to recognize self-antigens or fight infection or disease. In certain aspects, cell phenotype is identified by detecting and/or quantifying one or more markers on the cell surface or intracellularly, which readily enables identification of specific sub-types of cells of interest, which can then be analyzed for gene expression in order to assay cell function. In additional aspects, function of particular subsets of cells identified by cell surface markers is determined by detecting patterns of gene expression, expression of RNA or other markers, by detecting and/or quantifying transcription in the cell, by assaying DNA content, by assaying cell receptors, and/or by detecting the number and/or state of cellular organelles, receptors and/or transport systems.