Systems for multiplexed analysis of gene expression using coded RNA reporters. The coded RNA reporters are expressed from a library of reporter genes, with each reporter gene directing expression of a distinguishable coded RNA reporter. Each RNA reporter thus reports activity of a corresponding reporter gene. The distinguishable reporter RNA species allow otherwise similar reporter genes to be functionally linked to different effectors within a cell reporter library. Multiplexed analysis of reporter gene activity is carried out by measuring the level of each RNA reporter within the cell reporter library, thus providing an ability to analyze the effect of a biological modulator on many effectors.