The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains

The chromosomal position of human genes is rapidly being established. We integrated these mapping data with genome-wide messenger RNA expression profiles as provided by SAGE (serial analysis of gene expression). Over 2.45 million SAGE transcript tags, including 160,000 tags of neuroblastomas, are presently known for 12 tissue types. We developed algorithms to assign these tags to UniGene clusters and their chromosomal position. The resulting Human Transcriptome Map generates gene expression profiles for any chromosomal region in 12 normal and pathologic tissue types. The map reveals a clustering of highly expressed genes to specific chromosomal regions. It provides a tool to search for genes that are overexpressed or silenced in cancer.

[1]  W. Gardner,et al.  Carcinogenesis , 1961, The Yale Journal of Biology and Medicine.

[2]  J. Trent,et al.  Amplified DNA with limited homology to myc cellular oncogene is shared by human neuroblastoma cell lines and a neuroblastoma tumour , 1983, Nature.

[3]  Barbara L. Billington,et al.  Position effect at S. cerevisiae telomeres: Reversible repression of Pol II transcription , 1990, Cell.

[4]  B. van Steensel,et al.  Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus , 1993, The Journal of cell biology.

[5]  AC Tose.  Cell , 1993, Cell.

[6]  Wendy A. Bickmore,et al.  The distribution of CpG islands in mammalian chromosomes , 1994, Nature Genetics.

[7]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[8]  P. Lijnzaad,et al.  A physical map of 30,000 human genes. , 1998, Science.

[9]  E M Manders,et al.  Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. , 1998, Molecular biology of the cell.

[10]  S. Altschul,et al.  A public database for gene expression in human cancers. , 1999, Cancer research.

[11]  Ronald Berezney,et al.  Three-Dimensional Visualization of Transcription Sites and Their Association with Splicing Factor–Rich Nuclear Speckles , 1999, The Journal of cell biology.

[12]  G. Landes,et al.  Analysis of human transcriptomes , 1999, Nature Genetics.

[13]  Gen Tamiya,et al.  Complete sequence and gene map of a human major histocompatibility complex , 1999 .

[14]  M. Hattori,et al.  The DNA sequence of human chromosome 21 , 2000, Nature.