Updated project metadata. We investigated which signaling pathways downstream of Gas6/Axl promote the invasive phenotype of liver cancer cells. Thus, we performed phospho-proteomic analysis of MR hepatocytes and those expressing Axl (MR-Axl) in the presence and absence of Gas6. Protein-clustering based on the pattern of phosphorylation across the conditions and samples revealed four clusters: phospho-sites that are upregulated dependent on Axl expression (cluster 1) or Gas6 expression (cluster 2) and phospho-sites that are downregulated dependent on Axl expression (cluster 3) or Gas6 expression (cluster 4). Functional enrichment analysis showed enrichment of protein sets associated with cellular polarity and motility depending on changes in Axl expression and Gas6 activation. Furthermore, we analyzed phospho-proteomic data to estimate the activity of kinases based on kinase-substrate interactions using PhosR. Kinase perturbation analysis indicated mammalian target of rapamycin (mTOR) as the one with the highest upregulated activity in Gas6-stimulated MR-Axl cells compared to Gas6-stimulated MR cells. Accordingly, we analyzed substrates of mTOR and found that phosphorylation of Akt1 (Ser473) was upregulated in cluster 1 and highly increased in Gas6-stimulated MR-Axl, suggesting that Akt is regulated by Axl.