Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

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Identifying Novel Transcripts/Novel Genes in the Human Genome by Using Novel SAGE Tags

Jianjun Chen*, Miao Sun, Sanggyu Lee*, Guolin Zhou*, Janet D. Rowley*, San Ming Wang*
*Department of Medicine and Computer Science, University of Chicago,5841 S. Maryland, MC2115, Chicago, IL 60637
Telephone: (773) 702-6788
Fax: (773) 702-3002

One of the goals of human genome studies is to identify all the genes in the human genome for further functional analysis of each gene. However, the number of genes in the human genome remains a controversial issue. Whereas most of the genes in the human genome are said to have been physically or computationally identified, many short cDNA sequences identified as tags by use of SAGE (serial analysis of gene expression) do not match these genes. By performing experimental verification of more than 1,000 SAGE tags and analyzing 4,285,923 SAGE tags of human origin in the current SAGE database, we examined the nature of the unmatched SAGE tags. Our study shows that most of the unmatched SAGE tags are truly novel SAGE tags that originated from novel transcripts not yet identified in the human genome, including novel alternatively spliced transcripts from known genes and potential novel genes. Our study also indicates that by using GLGI (generation of longer cDNA fragments from SAGE tags for gene identification) and 5' RACE (rapid amplification of 5' cDNA ends), novel SAGE tags can be converted back to their corresponding 3' cDNAs and full-length cDNAs. By using such approach, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods, thus the rate of discovery of novel transcripts/novel genes in the human genome should be significantly accelerated. The same approach should also be applicable to gene identification in other eukaryotic genomes.

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