Cell migration is an essential process in health and disease - especially in cancer metastasis. The difficulty to assess migration in high throughput presents a methodological hurdle - hence, only very few screens revealed factors controlling this important process. Here, we introduce MigExpress as a platform for the "identification of Migration control genes by differential Expression". MigExpress exploits the combination of in-depth molecular profiling and the robust quantitative analysis of migration capacity in a broad panel of samples and identifies migration-associated genes by their differential expression in slowly versus fast migrating cells. We applied MigExpress to non-small cell lung cancer (NSCLC), the most frequent cause of cancer mortality mainly due to metastasis. In 54 NSCLC cell lines, we comprehensively determined mRNA and protein expression. Correlating the transcriptome and proteome profiles with the quantified migration properties led to the discovery and validation of FLNC, DSE, CPA4, TUBB6 and BICC1 as migration control factors in NSCLC cells, which also negatively correlated with patient survival. Notably, FLNC was the least expressed filamin in NSCLC, but the only one controlling cell migration and correlating with patient survival and metastatic disease stage.