A method of identifying candidate molecular mediators of parenchymal and non-parenchymal cell interactions, comprising: (a) obtaining a first co-culture of a parenchymal cell population and a first non-parenchymal cell population, measuring a tissue-specific function of the parenchymal cells and correlating the tissue-specific function with a gene expression profile of the first non-parenchymal cell population; (b) obtaining a second co-culture of the parenchymal cell population and a second non-parenchymal cell population, measuring the tissue-specific function of the parenchymal cells and correlating the tissue-specific function with a gene expression profile of the second non-parenchymal cell population; (c) generating a functional profile, comprising: (i) identifying a change in the induction of tissue-specific function resulting from co-culture of the parenchymal cell population with the first non-parenchymal cell population as compared to the second non-parenchymal cell population and scoring the non-parenchymal cell populations based on their relative induction of tissue-specific function; (ii) comparing the first and second gene expression profiles to identify a plurality of genes differentially expressed when comparing the profiles and selecting genes which stimulate or inhibit the tissue-specific function, wherein said genes are further selected from cell surface, matrix and secreted factors; and (iii) correlating the differential expression of the plurality of genes with the change in the induction of tissue- specific function; wherein the functional profile comprises the plurality of genes differentially expressed and selected according to (iii), and identifies the genes as candidate molecular mediators. (a) obtaining a first co-culture of a parenchymal cell population and a first non-parenchymal cell population, measuring a tissue-specific function of the parenchymal cells and correlating the tissue-specific function with a gene expression profile of the first non-parenchymal cell population; (b) obtaining a second co-culture of the parenchymal cell population and a second non-parenchymal cell population, measuring the tissue-specific function of the parenchymal cells and correlating the tissue-specific function with a gene expression profile of the second non-parenchymal cell population; (c) generating a functional profile, comprising: (i) identifying a change in the induction of tissue-specific function resulting from co-culture of the parenchymal cell population with the first non-parenchymal cell population as compared to the second non-parenchymal cell population and scoring the non-parenchymal cell populations based on their relative induction of tissue-specific function; (ii) comparing the first and second gene expression profiles to identify a plurality of genes differentially expressed when comparing the profiles and selecting genes which stimulate or inhibit the tissue-specific function, wherein said genes are further selected from cell surface, matrix and secreted factors; and (iii) correlating the differential expression of the plurality of genes with the change in the induction of tissue- specific function; wherein the functional profile comprises the plurality of genes differentially expressed and selected according to (iii), and identifies the genes as candidate molecular mediators. (i) identifying a change in the induction of tissue-specific function resulting from co-culture of the parenchymal cell population with the first non-parenchymal cell population as compared to the second non-parenchymal cell population and scoring the non-parenchymal cell populations based on their relative induction of tissue-specific function; (ii) comparing the first and second gene expression profiles to identify a plurality of genes differentially expressed when comparing the profiles and selecting genes which stimulate or inhibit the tissue-specific function, wherein said genes are further selected from cell surface, matrix and secreted factors; and (iii) correlating the differential expression of the plurality of genes with the change in the induction of tissue- specific function;