An essential question in human biology is how cells and tissues differ in gene 
and protein expression and how these differences delineate specific biological 
function. Here, we have performed a global analysis of both mRNA and protein 
levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based 
mass spectrometry analysis and antibody-based confocal microscopy. The study was 
performed in three functionally different human cell lines and based on the 
global analysis, we estimated the fractions of mRNA and protein that are cell 
specific or expressed at similar/different levels in the cell lines. A highly 
ubiquitous RNA expression was found with >60% of the gene products detected in 
all cells. The changes of mRNA and protein levels in the cell lines using SILAC 
and RNA ratios show high correlations, even though the genome-wide dynamic range 
is substantially higher for the proteins as compared with the transcripts. Large 
general differences in abundance for proteins from various functional classes 
are observed and, in general, the cell-type specific proteins are low abundant 
and highly enriched for cell-surface proteins. Thus, this study shows a path to 
characterize the transcriptome and proteome in human cells from different 
origins.