We performed a genome-wide analysis of transcriptional start sites (TSSs) in 
human genes by multifaceted use of a massively parallel sequencer. By analyzing 
800 million sequences that were obtained from various types of transcriptome 
analyses, we characterized 140 million TSS tags in 12 human cell types. Despite 
the large number of TSS clusters (TSCs), the number of TSCs was observed to 
decrease sharply with increasing expression levels. Highly expressed TSCs 
exhibited several characteristic features: Nucleosome-seq analysis revealed 
highly ordered nucleosome structures, ChIP-seq analysis detected clear RNA 
polymerase II binding signals in their surrounding regions, evaluations of 
previously sequenced and newly shotgun-sequenced complete cDNA sequences showed 
that they encode preferable transcripts for protein translation, and RNA-seq 
analysis of polysome-incorporated RNAs yielded direct evidence that those 
transcripts are actually translated into proteins. We also demonstrate that 
integrative interpretation of transcriptome data is essential for the selection 
of putative alternative promoter TSCs, two of which also have protein 
consequences. Furthermore, discriminative chromatin features that separate TSCs 
at different expression levels were found for both genic TSCs and intergenic 
TSCs. The collected integrative information should provide a useful basis for 
future biological characterization of TSCs.