From a global perspective,the abundance of protein—final product of gene expression—is only partly controlled by transcription or mRNA abundance,and mRNA translation has been increasingly recognized as another major element of gene expression regulation.Recent technology advances in ribosome profiling now allow quantifications of mRNA translation at the genome-wide level and single-codon resolution.To fill the gap between the transcriptomics and proteomics in cancer research,we took advantages of the cutting-edge ribosome profiling technique,and generated the first genome-wide survey of translational regulations in Hepatocellular Carcinoma (HCC).First,to systematically identify the genes that are differentially translated in tumors (different rates of translation) compared to their adjacent normal tissues,we developed an analysis pipeline,Xtail,tailored for the ribosome profiling data.By looking into the results of differential translation,we uncovered a series of biological processes that have been altered in tumors by means of translational regulations.In addition to the altered rates of translation,more types of dysregulations have been uncovered from our data.These include open reading frames (ORFs) from annotated long non-coding RNAs,alternative translation initiation sites of coding genes,upstream ORFs,abnormal initiation and pausing during elongation,etc.Taken together,our work provides the first comprehensive landscape of translational dysregulations in HCC tumors,which serves as a valuable resource for further study of the tumorigenesis machinery implemented at the level of gene translation.