Skip to main content

On the Comparison of Sets of Alternative Transcripts

  • Conference paper

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7292)

Abstract

Alternative splicing is pervasive among complex eukaryote species. For some genes shared by numerous species, dozens of alternative transcripts are already annotated in databases. Most recent studies compare and catalog alternate splicing events within or across species, but there is an urgent need to be able to compare sets of whole transcripts both manually and automatically.

In this paper, we propose a general framework to compare sets of transcripts that are transcribed from orthologous loci of several species. The model is based on the construction of a common reference sequence, and on annotations that allow the reconstruction of ancestral sequences, the identification of conserved events, and the inference of gains and losses of donor/acceptors sites, exons, introns and transcripts.

Our representation of sets of transcripts is straightforward, and readable by both humans and computers. On the other hand, the model has a precise, formal specification that insures its coherence, consistency and scalability. We give several examples, among them a comparison of 24 Smox gene transcripts across five species.

Keywords

  • Alternative Splice
  • Reference Sequence
  • Acceptor Site
  • Splice Event
  • Alternative Transcript

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (Canada)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (Canada)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (Canada)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bollina, D., Lee, B.T., Tan, T.W., Ranganathan, S.: ASGS: an alternative splicing graph web service. Nucleic Acids Res. 34, W444–W447 (2006)

    CrossRef  Google Scholar 

  2. Bonizzoni, P., Mauri, G., Pesole, G., Picardi, E., Pirola, Y., Rizzi, R.: Detecting alternative gene structures from spliced ESTs: a computational approach. J. Comput. Biol. 16, 43–66 (2009)

    CrossRef  MathSciNet  Google Scholar 

  3. Carninci, P., Kasukawa, T., Katayama, S., et al.: The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005)

    CrossRef  Google Scholar 

  4. Christinat, Y., Moret, B.M.E.: Inferring transcript phylogenies. In: Proc. of IEEE International Conference on Bioinformatics and Biomedecine, pp. 208–215 (2011)

    Google Scholar 

  5. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the encode pilot project. Nature  447, 799–816 (2007)

    Google Scholar 

  6. Fitch, W.M.: Toward defining the course of evolution: minimum change for a specified tree topology. Systematic Zoology 20(4), 406–416 (1971)

    CrossRef  Google Scholar 

  7. Flicek, P., Amode, M.R., Barrell, D., et al.: Ensembl 2011. Nucleic Acids Res. 39, D800–D806 (2011)

    CrossRef  Google Scholar 

  8. Heber, S., Alekseyev, M., Sze, S.H., Tang, H., Pevzner, P.A.: Splicing graphs and EST assembly problem. Bioinformatics 18(suppl.1), S181–S188 (2002)

    CrossRef  Google Scholar 

  9. Lacroix, V., Sammeth, M., Guigo, R., Bergeron, A.: Exact Transcriptome Reconstruction from Short Sequence Reads. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 50–63. Springer, Heidelberg (2008)

    CrossRef  Google Scholar 

  10. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, A., Wilm, I.M., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G.: Clustal w and clustal x version 2.0. Bioinformatics 23, 2947–2948 (2007)

    CrossRef  Google Scholar 

  11. Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F., Dietz, H.C.: Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nature Genetics 36, 1073–1078 (2004)

    CrossRef  Google Scholar 

  12. Mudge, J.M., Frankish, A., Fernandez-Banet, J., Alioto, T., Derrien, T., Howald, C., Reymond, A., Guigo, R., Hubbard, T., Harrow, J.: The origins, evolution and functional potential of alternative splicing in vertebrates. Molecular Biology and Evolution 28, 2949–2959 (2011)

    CrossRef  Google Scholar 

  13. Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M., Gotoh, O.: Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics 22(10), 1211–1216 (2006)

    CrossRef  Google Scholar 

  14. Pavesi, G., Zambelli, F., Caggese, C., Pesole, G.: Exalign: a new method for comparative analysis of exon-intron gene structures. Nucleic Acids Res. 36, e47 (2008)

    CrossRef  Google Scholar 

  15. Pruitt, K.D., Harrow, J., Harte, R.A., et al.: The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 19, 1316–1323 (2009)

    CrossRef  Google Scholar 

  16. Sammeth, M., Foissac, S., Guigo, R.: A general definition and nomenclature for alternative splicing events. PLoS Computational Biology 8, e1000147 (2008)

    CrossRef  Google Scholar 

  17. Sammeth, M., Valiente, G., Guigo, R.: Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 372–395. Springer, Heidelberg (2008)

    CrossRef  Google Scholar 

  18. Zambelli, F., Pavesi, G., Gissi, C., Horner, D.S., Pesole, G.: Assessment of orthologous splicing isoforms in human and mouse orthologous genes. BMC Genomics 11, 534 (2010)

    CrossRef  Google Scholar 

  19. Zavolan, M., van Nimwegen, E.: The types and prevalence of alternative splice forms. Curr. Opin. Struct. Biol. 16, 362–367 (2006)

    CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ouangraoua, A., Swenson, K.M., Bergeron, A. (2012). On the Comparison of Sets of Alternative Transcripts. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_19

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-30191-9_19

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30190-2

  • Online ISBN: 978-3-642-30191-9

  • eBook Packages: Computer ScienceComputer Science (R0)