Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis.
Genes up-regulated in tumor cells provide attractive anticancer therapeutic targets. Although the general underlying mechanism for the increased expression in tumors is unknown, tumor-specific up-regulation of some genes can be attributed to aberrant DNA amplification, a phenomenon common to many tumors. Using a computational method, we constructed a general transcriptome map with the human genomic sequences and expressed sequence tags in the public database. The transcriptome map revealed nonrandom chromosomal regions (termed region of increased tumor expression) where clusters of genes exhibited increased expression in the 10 tumor tissue types tested. These genomic regions often correspond to experimentally verified tumor amplicons. Our large-scale transcriptome analysis led to identification of many additional chromosomal regions with increased tumor expression, regions that represent potential tumor amplicons.
Zhou
Yan
Y
Department of Bioinformatics, Genentech, Inc., South San Francisco, California 94080, USA.
Luoh
Shiuh-Ming
SM
Zhang
Yan
Y
Watanabe
Colin
C
Wu
Thomas D
TD
Ostland
Michael
M
Wood
William I
WI
Zhang
Zemin
Z
D002877:Chromosomes, Human / Q000235:genetics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D005810:Multigene Family; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D009693:Nucleic Acid Hybridization; D014158:Transcription, Genetic; D015854:Up-Regulation