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Analysis of human transcriptomes

Nature Genetics volume 23, pages 387–388 (1999)Cite this article

How many human genes are expressed ubiquitously, in all human tissues, and how many are expressed in tissue-specific patterns? To answer these fundamental questions in molecular biology, we have analysed 3.5-million transcripts from 19 normal and diseased tissue types. We found that as many as 43,500 genes can be expressed in a single cell type. Only a small fraction of transcripts were exclusively expressed in any individual tissue, whereas nearly 1,000 genes were expressed in all cell types examined. We found 40 genes to be expressed at elevated levels in all cancer tissues but not in normal cells.

Serial analysis of gene expression (SAGE) studies1,2 of 84 libraries derived from 19 different sources identified 134,135 transcripts from approximately 84,000 different genes (Table 1; data and analysis available at http://genetics.nature.com/supplementary_info/). Expression levels for these genes ranged from 0.3 to 9,417 transcript copies per cell. The transcript tags matched approximately 4,300 known genes and 41,000 genes with unknown functions, whereas the remaining transcript tags (46%) had no matches to existing databases (Table 2, see http://genetics.nature.com/supplementary_info/).

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Figure 1: Sampling of gene expression in colon cancer cells.

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Acknowledgements

We thank B. Wentworth, D. Jefferson and S.J. de Beur for providing tissues and cell lines; G. Schuler and L. Wagner for their work with the UniGene project; and D. Velculescu for assistance with Monte Carlo simulations. We thank members of our laboratories for useful advice and discussions. This research was supported by NIH grants CA57345, CA62924 and CA43460. B.V. is an investigator of the Howard Hughes Medical Institute. K.W.K. received research funding from Genzyme Molecular Oncology.

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Authors and Affiliations

  1. The Johns Hopkins Oncology Center, Baltimore , Maryland, USA

    Victor E Velculescu, Lin Zhang, Jian Yu, Anne T Ferguson, Tong-Chuan He, Paul M Hwang, Leigh Zawel, Wei Zhou, Saraswati Sukumar, Bert Vogelstein & Kenneth W Kinzler

  2. The Howard Hughes Medical Institute, Baltimore , Maryland, USA

    Carlo Rago, Heiko Hermeking, Paul M Hwang, Leigh Zawel, Wei Zhou & Bert Vogelstein

  3. Division of Cardiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Paul M Hwang

  4. Division of Otolaryngology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Jin Jen

  5. Genzyme Molecular Oncology, Framingham, Massachusetts, USA

    Stephen L Madden, Clarence J Wang, Gary A Beaudry, Kristin M Ciriello, Brian P Cook, Michael R Dufault, Yuhong Gao, Siewleng K Hiraldo, Marissa A Lopez, Hilary F Luderer, Brynna Mathews, Joseph M Petroziello, Wen Zhang, Xiaoming Zhang & Gregory M Landes

  6. National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA

    Alex E Lash

  7. Department of Pathology, Duke Univerisity School of Medicine, Durham, North Carolina, USA

    Anita Lal & Gregory J Riggins

  8. Department of Adult Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Kornelia Polyak

  9. Division of Hematology/Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA

    Frank G Haluska

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Correspondence to Victor E Velculescu.

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Velculescu, V., Madden, S., Zhang, L. et al. Analysis of human transcriptomes. Nat Genet 23, 387–388 (1999). https://doi.org/10.1038/70487

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