What transcripts are found in a human cell?

A total of 3.5 million transcripts was analyzed from 19 tissues (both normal and diseased, mainly cancer cell lines or primary tumor samples). From this, the number of genes in the human genome was estimated at around 84,000. The average number of different but related transcripts corresponding to each gene is 1.6 (134,135 transcripts total, mainly due to differences in polyadenylation). More than 43,000 transcripts were expressed in a single cell type (colorectal cancer cell lines) with expression levels ranging from 0.3 to 9,417 copies of the transcript per cell. Of the transcripts, 83% were present at levels as low as one copy per cell; 55 transcripts present at over 500 copies per cell made up 18% of the cellular mRNA mass (Figure 1a); and the most highly expressed 633 genes accounted for 45% of the cellular mRNA. Most unique transcripts were produced at low levels, with just under 25% of the cellular mRNA mass being made up of 94% of the unique transcripts (Figure 1b). Approximately 9,000 genes of known function and 63,000 genes of unknown function were matched to the transcripts; the remaining transcript tags, mainly from genes expressed at a low level (46%), had no matches in existing (public) databases (Figure 1c). Differences in gene expression between different cell types were greater than the changes in gene expression observed in different physiological states of a given cell type. Expression levels of tissue-specific transcripts present at more than ten copies per cell ranged from 0.05% to 1.76% (as a percentage of total cellular mRNA), and 50% of these transcripts had no database match. Approximately 1,000 'ubiquitously' expressed transcripts were detected and may be viewed as a minimal transcriptome.More information about SAGE is available from the Serial analysis of gene expression homepage and the SAGEmap site at the National Center for Biotechnological Information (NCBI). For information on cDNA microarray technology visit the Gene Chips (DNA Micro