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PMID: 12213963 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 99 ·No. 19 ·2002-09-17 ·Pages 12257-62

Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM

Abstract

The number of genes in the human genome is still 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 serial analysis of gene expression (SAGE) 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 alternatively spliced transcripts from known genes and potential novel genes. Our study indicates that by using novel SAGE tags as probes, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods.

MeSH Terms
Base Pair Mismatch Base Sequence DNA, Complementary/genetics Databases, Nucleic Acid Expressed Sequence Tags Gene Expression Profiling Genome, Human Humans Molecular Sequence Data Sequence Tagged Sites Transcription, Genetic
Chemicals
DNA, Complementary
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Chen Jianjun
Department of Medicine, University of Chicago, 5841 South Maryland, MC2115, Chicago, IL 60637, USA.
Sun Miao
Lee Sanggyu
Zhou Guolin
Rowley Janet D
Wang San Ming
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.192436499
Published
2002-09-17
Epub
2002-00-04
Pages
12257-62
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC129432
Subset
IM
Grants
NCI NIH HHS · R01 CA084405 · United States
NCI NIH HHS · CA84405 · United States
Databases
GENBANK
BM285378, BM285379, BM285380, BM285381, BM285382, BM285383, BM285384, BM285385, BM285386, BM285387, BM285388, BM285389, BM285390, BM285391, BM285392, BM285393, BM285394, BQ635328, BQ635329, BQ635330, BQ635331, BQ635332
External Links
PubMed source DOI: 10.1073/pnas.192436499 PMC Full Text View journal details
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