SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions
Open accessAbstract
Serial analysis of gene expression (SAGE) not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery of novel transcripts. SAGE tags are mapped to known transcripts to determine the gene of origin. Tags that map neither to a known transcript nor to the genome were hypothesized to span a splice junction, for which the exon combination or exon(s) are unknown. To test this hypothesis, we have developed an algorithm, SAGE2Splice, to efficiently map SAGE tags to potential splice junctions in a genome. The algorithm consists of three search levels. A scoring scheme was designed based on position weight matrices to assess the quality of candidates. Using optimized parameters for SAGE2Splice analysis and two sets of SAGE data, candidate junctions were discovered for 5%-6% of unmapped tags. Candidates were classified into three categories, reflecting the previous annotations of the putative splice junctions. Analysis of predicted tags extracted from EST sequences demonstrated that candidate junctions having the splice junction located closer to the center of the tags are more reliable. Nine of these 12 candidates were validated by RT-PCR and sequencing, and among these, four revealed previously uncharacterized exons. Thus, SAGE2Splice provides a new functionality for the identification of novel transcripts and exons. SAGE2Splice is available online at http://www.cisreg.ca.
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The 44 unmapped tag-sequences may span an unknown splice junction.
“For example, these 44 tag-sequences may span an unknown splice junction [37].”
From A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE) (2007) · cites this paper as [37]
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Cites
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993 · see citing works
Base-Calling of Automated Sequencer Traces Using <i>Phred.</i> II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439 · see citing works
Organization and Expression of Eucaryotic Split Genes Coding for Proteins
Breathnach, R., & Chambon, P. (1981) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.50.070181.002025 · Cited by 4,649 · see citing works
Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441 · see citing works
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 · see citing works
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 · see citing works
Biological sequence analysis probabilistic models of proteins and nucleic acids
Durbin, R. M., Eddy, S. R., Krogh, A., & Mitchison, G. (1998) · Cited by 3,565 · see citing works
Pruitt, K., Tatusova, T., & Maglott, D. (2004) · Nucleic Acids Res. · doi:10.1093/nar/gki025 · Cited by 3,248 · see citing works
The UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,887 · see citing works
DNA binding sites: representation and discovery
Stormo, G. D. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.1.16 · Cited by 1,519 · see citing works
A genomic view of alternative splicing
Modrek, B., & Lee, C. (2002) · Nature Genetics · doi:10.1038/ng0102-13 · Cited by 1,307 · see citing works
Prediction of human mRNA donor and acceptor sites from the DNA sequence
Brunak, S., Engelbrecht, J., & Knudsen, S. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90380-o · Cited by 794 · see citing works
Using the transcriptome to annotate the genome
Saha, S., Sparks, A. B., Rago, C., Akmaev, V., Wang, C. J., Vogelstein, B., Kinzler, K. W., & Velculescu, V. E. (2002) · Nature Biotechnology · doi:10.1038/nbt0502-508 · Cited by 630 · see citing works
Analysis of canonical and non-canonical splice sites in mammalian genomes
Burset, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.21.4364 · Cited by 616 · see citing works
Frequent Alternative Splicing of Human GenesPreprint
Mironov, A. A., Fickett, J. W., & Gelfand, M. S. (1999) · Genome Research · doi:10.1101/gr.9.12.1288 · Cited by 549 · see citing works
Integrating genomic homology into gene structure prediction
Korf, I. F., Flicek, P., Duan, D., & Brent, M. R. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.suppl_1.s140 · Cited by 467 · see citing works
SAGEmap: A Public Gene Expression ResourcePreprint
Lash, A., Tolstoshev, C. M., Wagner, L., Schuler, G. D., Strausberg, R. L., Riggins, G. J., & Altschul, S. F. (2000) · Genome Research · doi:10.1101/gr.10.7.1051 · Cited by 418 · see citing works
Intron—exon structures of eukaryotic model organisms
Long, M., & Deutsch, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.15.3219 · Cited by 417 · see citing works
Guigó, R., Knudsen, S., Drake, N. L., & Smith, T. F. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90130-c · Cited by 379 · see citing works
An anatomy of normal and malignant gene expression
Boon, K., Osório, E. C., Greenhut, S. F., Schaefer, C. F., Shoemaker, J. S., Polyák, K., Morin, P. J., Buetow, K. H., Strausberg, R. L., SOUZA, S. J. D., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.152324199 · Cited by 304 · see citing works
Strausberg, R. L., Feingold, E. A., Klausner, R. D., & Collins, F. S. (1999) · Science · doi:10.1126/science.286.5439.455 · Cited by 287 · see citing works
Jones, S. J. M., Riddle, D. L., Pouzyrev, A. T., Velculescu, V. E., Hillier, L., Eddy, S. R., Stricklin, S. L., Baillie, D. L., Waterston, R., & Marra, M. A. (2001) · Genome Research · doi:10.1101/gr.184401 · Cited by 227 · see citing works
A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death
Gorski, S. M., Chittaranjan, S., Pleasance, E. D., Freeman, J. D., Anderson, C. L., Varhol, R. J., Coughlin, S. M., Zuyderduyn, S. D., Jones, S. J. M., & Marra, M. A. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00082-4 · Cited by 213 · see citing works
Analysing uncharted transcriptomes with SAGE
Velculescu, V. E., Vogelstein, B., & Kinzler, K. W. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02114-4 · Cited by 213 · see citing works
[13] Consensus patterns in DNA
Stormo, G. D. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83015-2 · Cited by 204 · see citing works
Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags
Chen, J., Sun, M., Lee, S., Zhou, G., Rowley, J. D., & Wang, S. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192436499 · Cited by 155 · see citing works
Siddiqui, A. S., Khattra, J., Delaney, A. D., Zhao, Y., Astell, C., Asano, J., Babakaiff, R., Barber, S., Beland, J., Bohacec, S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509455102 · Cited by 116 · see citing works
Self-citationYajima, I., Sato, S., Kimura, T., Yasumoto, K., Shibahara, S., Goding, C. R., & Yamamoto, H. (1999) · Human Molecular Genetics · doi:10.1093/hmg/8.8.1431 · Cited by 113 · see citing works
Inventory of High-Abundance mRNAs in Skeletal Muscle of Normal MenPreprint
Welle, S. L., Bhatt, K. S., & Thornton, C. A. (1999) · Genome Research · doi:10.1101/gr.9.5.506 · Cited by 112 · see citing works
SGP-1: Prediction and Validation of Homologous Genes Based on Sequence AlignmentsPreprint
Wiehe, T., Gebauer-Jung, S., Mitchell‐Olds, T., & Guigó, R. (2001) · Genome Research · doi:10.1101/gr.177401 · Cited by 106 · see citing works
Assessment of SAGE in Transcript IdentificationPreprint
Pleasance, E., Marra, M. A., & Jones, S. J. M. (2003) · Genome Research · doi:10.1101/gr.873003 · Cited by 74 · see citing works
Serial analysis of gene expression: from gene discovery to target identification
Madden, S. L., Wang, C. J., & Landes, G. M. (2000) · Drug Discovery Today · doi:10.1016/s1359-6446(00)01544-0 · Cited by 69 · see citing works
The new role of SAGE in gene discovery
Boheler, K. R., & Stern, M. D. (2003) · Trends in biotechnology · doi:10.1016/s0167-7799(02)00031-8 · Cited by 45 · see citing works
Keime, C., Damiola, F., Mouchiroud, D., Duret, L., & Gandrillon, O. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-143 · Cited by 23 · see citing works
The Mouse SAGE Site: database of public mouse SAGE libraries
Divina, P. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh058 · Cited by 20 · see citing works
Analysis of a human brain transcriptome map
Qiu, P., Benbow, L., Liu, S., Greene, J. R., & Wang, L. (2002) · BMC Genomics · doi:10.1186/1471-2164-3-10 · Cited by 19 · see citing works
Generation of Longer cDNA Fragments from SAGE Tags for Gene Identification
Chen, J., Lee, S., Zhou, G., Rowley, J. D., & Wang, S. M. (2003) · Humana Press eBooks · doi:10.1385/1-59259-359-3:207 · Cited by 6 · see citing works
Flagged first, then by citations
1 of the 38 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Hou, J., Charters, A. M., Lee, S. C., Zhao, Y., Wu, M. K., Jones, S. J., Marra, M. A., & Hoodless, P. A. (2007) · BMC Developmental Biology · doi:10.1186/1471-213x-7-92 · Cited by 56 · see citing works
“For example, these 44 tag-sequences may span an unknown splice junction [37].”
BackgroundAnalysis of wheat SAGE tags reveals evidence for widespread antisense transcription
Poole, R. L., Barker, G., Werner, K., Biggi, G. F., Coghill, J. A., Gibbings, J. G., Berry, S. T., Dunwell, J. M., & Edwards, K. J. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-475 · Cited by 25 · see citing works
Brownian self-driven particles on the surface of a sphere
Apaza, L., & Sandoval, M. (2017) · Physical review. E · doi:10.1103/physreve.96.022606 · Cited by 25 · see citing works
Active matter on Riemannian manifolds
Apaza, L., & Sandoval, M. (2018) · Soft Matter · doi:10.1039/c8sm01034j · Cited by 23 · see citing works
Binary mixtures of active and passive particles on a sphere
Ai, B.-Q., Zhou, B.-Y., & Zhang, X. (2020) · Soft Matter · doi:10.1039/d0sm00281j · Cited by 17 · see citing works
Deep SAGE analysis of the Caenorhabditis elegans transcriptome
Ruzanov, P., & Riddle, D. L. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq035 · Cited by 16 · see citing works
Collective transport of polar active particles on the surface of a corrugated tube
Ai, B.-Q., Zhu, W.-J., & Liao, J. (2019) · New Journal of Physics · doi:10.1088/1367-2630/ab3fc5 · Cited by 13 · see citing works
Ruzanov, P., Jones, S. J. M., & Riddle, D. L. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-447 · Cited by 11 · see citing works
MultiPriDe: automated batch development of quantitative real-time PCR primers
Ziesel, A., Chrenek, M. A., & WONG, P. W. K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn165 · Cited by 2 · see citing works
One-dimensional displacement of active matter on curved substrates
Herrera, P., Apaza, L., & Sandoval, M. (2020) · Molecular Physics · doi:10.1080/00268976.2020.1711974 · Cited by 2 · see citing works
Computational Analysis of SAGE Data
Seeja, K. R. (2012) · LAP LAMBERT Academic Publishing eBooks
Inertial and confined dynamics of a constant-speed active particle in three dimensions
Rodriguez, G., Rangaig, M. T., & Rangaig, N. A. (2025) · Physical review. E · doi:10.1103/11k8-jyp5
- Authors
- Kuo, B. Y.-L., Chen, Y., Bohacec, S., Johansson, Ö., Wasserman, W. W., & Simpson, E. M.
- Affiliations
- University of British Columbia (CA)
- AlbaNova (SE)
- Corresponding author
- Simpson, Elizabeth M
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2006-04-28
- Volume
- 2
- Issue
- 4
- Pages
- e34
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC1447652
- OpenAlex
- W2023809988
- Cited by
- 12
- References
- 38
- Citations by year
- 2025: 1 · 2020: 2 · 2019: 1 · 2018: 1 · 2017: 1 · 2012: 1
- FWCI
- 0.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- cIRcle (University of British Columbia) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Genome Canada
- Michael Smith Health Research BC
- Genome British Columbia
- Canadian Institutes of Health Research (69153)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- 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
- Keywords
- serial analysis of gene expression, SAGE tags, novel exons, novel transcripts, position weight matrices, expressed sequence tags
- MeSH terms
- Algorithms, Animals, Base Sequence, Introns, Models, Genetic, Molecular Sequence Data, Sensitivity and Specificity, Gene Expression Profiling, RNA Splice Sites, Mice
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