Conditioned media (CM) of transformed cells, such as the human lung-derived A549 cells, is a useful tool for directing differentiation of embryonic stem cells (ESCs). Previous work indicates that A549-CM induced pulmonary differentiation of mouse ESCs (mESCs). In this study, we compared the effects of A549-CM treatment on the differentiation of mESCs organized in monolayer or embryoid bodies. We analyzed the cultures treated with A549-CM using specific lineage markers by quantitative polymerase chain reaction (qPCR) and lineage-focused PCR arrays and demonstrated heterogeneous CM-induced differentiation. We then constructed bioinformatics-based gene networks to establish correlations between the upregulated lineage-specific genes and proteins in the A549-CM identified by proteomic analysis. Network analysis supported the phenotypic and genotypic heterogeneic differentiation of mESCs into multiple cell lineages via enriched stemness, cardiovascular, neuronal, and lung development gene ontologies (GOs). The significant enrichment toward lung ontologies was specific for treatment with A549-CM, but not CM of liver (HepG2) and pancreas (Capan-1) cells. Based on network analysis, we identified laminin alpha5, prosaposin, lamin A/C, dickkopf homolog 1, clusterin, and calreticulin as the most relevant proteins related to the enrichment of lung GOs. We validated the effects of laminin isoforms on mESC differentiation in vitro and found enriched differential induction of surfactant protein gene expression. Our data suggest that A549-CM can be used for identifying secreted proteins for the heterogeneous mixed-lineage differentiation of mESCs toward a variety of lung-relevant cells. Such a heterogeneous cell population will be required for the in vitro generation of complex lung tissue and mixed cell populations for regenerative pulmonary therapy.