The DOI matches its Crossref record; 19 of the 20 references it cites were found in a registry or an index.
Using the transcriptome to annotate the genome
Abstract
A remaining challenge for the human genome project involves the identification and annotation of expressed genes. The public and private sequencing efforts have identified approximately 15,000 sequences that meet stringent criteria for genes, such as correspondence with known genes from humans or other species, and have made another approximately 10,000-20,000 gene predictions of lower confidence, supported by various types of in silico evidence, including homology studies, domain searches, and ab initio gene predictions. These computational methods have limitations, both because they are unable to identify a significant fraction of genes and exons and because they are unable to provide definitive evidence about whether a hypothetical gene is actually expressed. As the in silico approaches identified a smaller number of genes than anticipated, we wondered whether high-throughput experimental analyses could be used to provide evidence for the expression of hypothetical genes and to reveal previously undiscovered genes. We describe here the development of such a method--called long serial analysis of gene expression (LongSAGE), an adaption of the original SAGE approach--that can be used to rapidly identify novel genes and exons.
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“SAGE has been improved by the development of a longSAGE protocol, which generates tags that are 21 bp long and provides enhanced efficiency and accuracy of tag-to-gene mapping [30-32].”
From A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE) (2007) · cites this paper as [31]
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Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Prediction of complete gene structures in human genomic DNA
Burge, C., & Karlin, S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0951 · Cited by 4,211
Serial Analysis of Gene Expression
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995) · Science · doi:10.1126/science.270.5235.484 · Cited by 3,713
Self-citationA model for p53-induced apoptosis
Polyak, K., Xia, Y., Zweier, J. L., Kinzler, K. W., & Vogelstein, B. (1997) · Nature · doi:10.1038/38525 · Cited by 2,500
Self-citationThe DNA sequence of human chromosome 22
Dunham, I., Hunt, A. R., Collins, J. E., Bruskiewich, R., Beare, D. M., Clamp, M. E., Smink, L. J., Ainscough, R., Almeida, J. P., Babbage, A., et al. (1999) · Nature · doi:10.1038/990031 · Cited by 1,147
Adams, Kerlavage, A. R., Fleischmann, R. D., Ra, F., Cj, B., Lee, N., Ef, K., Kg, W., Gocayne, J. D., & White, O. R. (1995) · PubMed · Cited by 793
Analysis of human transcriptomes
Velculescu, V. E., Madden, S. L., Zhang, L., Lash, A., Yu, J., Rago, C., Lal, A., Wang, C. J., Beaudry, G. A., Ciriello, K. M., et al. (1999) · Nature Genetics · doi:10.1038/70487 · Cited by 775
Self-citationThe Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains
Caron, H. N., van Schaik, B. D. C., van der Mee, M., Baas, F., Riggins, G. J., Sluis, P. V., Hermus, M.-C., van Asperen, R., Boon, K., Voûte, P. A., et al. (2001) · Science · doi:10.1126/science.1056794 · Cited by 730
Experimental annotation of the human genome using microarray technology
Shoemaker, D. D., Schadt, E. E., Armour, C. D., He, Y. D., Garrett-Engele, P. W., MCDONAGH, P. D., Loerch, P., Leonardson, A. S., Lum, P. Y., Cavet, G., et al. (2001) · Nature · doi:10.1038/35057141 · Cited by 440
Cited by
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Greenbaum, D. S., & Claverie, J. (2004) · Dictionary of Bioinformatics and Computational Biology · doi:10.1002/9780471650126.dob0752.pub2
(2002) · Handbook of immunohistochemistry and in situ hybridization of human carcinomas · doi:10.1016/s1874-5784(04)80008-4
Upadhyaya, N. M., & Dennis, E. S. (2009) · Springer eBooks · doi:10.1007/978-90-481-2967-6_11
Wei, C., & Ruan, Y. (2009) · Pan Stanford Publishing eBooks · doi:10.1201/b11146-5
Principles and techniques in molecular biology
Remmers, E. F., Ombrello, M. J., Kanno, Y., Siegel, R. M., & Kastner, D. L. (2011) · Elsevier eBooks · doi:10.1016/b978-0-323-06551-1.00012-9
New Era of Genome-Wide Gene Expression Analysis
Maeda, N. (2009) · Pan Stanford Publishing eBooks · doi:10.1201/b11146-6
Blackshaw, S. (2005) · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics · doi:10.1002/047001153x.g208414
(2005) · Handbook of immunohistochemistry and in situ hybridization of human carcinomas · doi:10.1016/s1874-5784(05)80005-4
Zhang, C., Li, Y., Wang, X., Zhang, L., Li, X., Wang, Y., & Xu, S. (2009) · Genetic Testing · doi:10.1089/gte.2008.0078
Complexity in Systems Level Biology and Genetics: Statistical Perspectives
Stephens, D. A. (2011) · Springer eBooks · doi:10.1007/978-1-4614-1800-9_36
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Stephens, D. A. (2009) · Encyclopedia of Complexity and Systems Science · doi:10.1007/978-0-387-30440-3_82
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Terauchi, R., Win, J., Kamoun, S., Matsumura, H., Saitoh, H., Kanzaki, H., Yoshida, K., Shenton, M., Berberich, T., Fujisawa, S., et al. (2009) · Springer eBooks · doi:10.1007/978-1-4020-9500-9_11
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Stein, W. D., Litman, T., Fojo, T., & Bates, S. E. (2023) · doi:10.1158/0008-5472.c.6493706
Álvarez, H., Corvalán, A. H., Roa, J. C., Argani, P., Murillo, F., Edwards, J., Beaty, R. M., Feldmann, G., Hong, S., Mullendore, M. E., et al. (2023) · doi:10.1158/1078-0432.c.6516931.v1
Huang, T., Yang, M., Dong, K., Xu, M., Liu, J., Chen, Z., Zhu, S., Chen, W., Yin, J., Jin, K., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11986701
Huang, T., Yang, M., Dong, K., Xu, M., Liu, J., Chen, Z., Zhu, S., Chen, W., Yin, J., Jin, K., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11986728
Huang, T., Yang, M., Dong, K., Xu, M., Liu, J., Chen, Z., Zhu, S., Chen, W., Yin, J., Jin, K., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11986722
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Huang, T., Yang, M., Dong, K., Xu, M., Liu, J., Chen, Z., Zhu, S., Chen, W., Yin, J., Jin, K., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11986710
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Ma, X., Ren, Y., He, J., Zhang, L., Cui, H., Liu, Y. N., Huang, J., Wang, A., & Liang, B. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-14170-6.00037-8
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Tang, A. Y., & Ling, M. H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00225-6
Pramanik, S., Seth, D., Das, A., & Debnath, S. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-33341-5.00015-x
Tag-based amplification of cDNA ends: a new approach to gene discovery
Nesbitt, M. J. (2009) · Summit (Simon Fraser University)
Huang, T., Yang, M., Dong, K., Xu, M., Liu, J., Chen, Z., Zhu, S., Chen, W., Yin, J., Jin, K., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11986716
Caractérisation de la reprogrammation de l'expression des gènes chez les blés allopyloïdes
Chalabi, S. (2014) · theses.fr (ABES) · doi:10.70675/bee96c14z587dz44d5zad96z53a7d6126cec
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Xia, X. (2026) · Springer eBooks · doi:10.1007/978-3-032-18842-7_4
BLAST, FASTA, and String Algorithms
Xia, X. (2026) · Springer eBooks · doi:10.1007/978-3-032-18842-7_1
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Metadata
- Authors
- Saha, S., Sparks, A. B., Rago, C., Akmaev, V., Wang, C. J., Vogelstein, B., Kinzler, K. W., & Velculescu, V. E.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Kinzler, Kenneth W.
- Velculescu, Victor E.
- Venue
- Nature Biotechnology
- Published
- 2002-05
- Volume
- 20
- Issue
- 5
- Pages
- 508-512
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2002982210
- Cited by
- 630
- References
- 20
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 3 · 2023: 6 · 2022: 6 · 2021: 4 · 2020: 7 · 2019: 14 · 2018: 18 · 2017: 6 · 2016: 8 · 2015: 15 · 2014: 14 · 2013: 15 · 2012: 24
- FWCI
- 19.47
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Cancer Institute (CA 57345)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- LongSAGE, serial analysis of gene expression, transcriptome, genome annotation, gene discovery, exon identification, expressed genes, human genome annotation, sage
- MeSH terms
- Genetic Techniques, Humans, Models, Genetic, RNA, Messenger, Software, Human Genome Project, Genome, DNA, Complementary, Reverse Transcriptase Polymerase Chain Reaction
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