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A Web Resource on Skeletal Muscle Transcriptome of Primates

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Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9874))

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Abstract

Skeletal muscle represents a very well organized anatomical tissue in animals and its appearance might have predated the divergence of vertebrate and arthropods lineages about 700MYA. This diversified structure is very well visible in Primates since it differentiates according to their life styles and environmental conditions. This study focuses on Pan troglodytes - known as common chimpanzee - which belongs to a genus that is the most closely related to human species by which also shares a high similarity in the DNA composition. Our aim is to test the level of similarity between chimpanzee and human DNA - diversified to a functional phenotypic level to better adapt in different environmental conditions - by collecting skeletal muscle transcriptomic data from ENA (European Nucleotide Archive) database and performing its functional annotation analysis. We developed PrimatesDB, a freely available web-oriented application which contains 30,944 sequences belonging to Pan troglodytes skeletal muscle transcriptomic data and from which it is possible to retrieve all the information related to 12,222 transcripts. PrimatesDB is available at: www-labgtp.na.icar.cnr.it/PrimatesDB.

D. Evangelista and M. Avino—Contributed equally to this work.

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References

  1. Steinmetz, P.R.H., Kraus, J.E.M., Larroux, C., Hammel, J.U., Amon-Hassenzahl, A., Houliston, E., Wrheide, G., Nickel, M., Degnan, B.M., Technau, U.: Independent evolution of striated muscles in cnidarians and bilaterians. Nature 487(7406), 231–234 (2012)

    Article  Google Scholar 

  2. Ankel-Simons, F.: Primate Anatomy: An Introduction. Academic Press, New York (2000)

    Google Scholar 

  3. Fleagle, J.G.: Primate Adaptation and Evolution. Academic Press, New York (1988)

    Google Scholar 

  4. Maudhoo, M.D., Madison, J.D., Norgren, R.B.: De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences. GigaScience 4(1), 1–4 (2015)

    Article  Google Scholar 

  5. Wilson, D.E., Reeder, D.M.: Pan troglodytes. In: Mammal Species of the World: A Taxonomic and Geographic Reference. Johns Hopkins University Press, 3rd edn. (2005)

    Google Scholar 

  6. Martin, R.D.: Primate Origins, Evolution: A Phylogenetic Reconstruction. Princeton University Press, Princeton (1990)

    Google Scholar 

  7. Bukh, J.: A critical role for the chimpanzee model in the study of hepatitis C. Hepatology 39(6), 1469–75 (2004)

    Article  Google Scholar 

  8. de Groot, N.G., Bontrop, R.E.: The HIV-1 pandemic: does the selective sweep in chimpanzees mirror humankind’s future. Retrovirology 10(1), 53 (2013)

    Article  Google Scholar 

  9. The Chimpanzee Sequencing and Analysis Consortium: Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437(7055), 69–87 (2005)

    Google Scholar 

  10. Perelman, P., et al.: A molecular phylogeny of living primates. PLoS Genet. 7, 3 (2011)

    Article  Google Scholar 

  11. MacPhee, R.D. (ed.): Primates and Their Relatives in Phylogenetic Perspective. Springer, Heidelberg (2013)

    Google Scholar 

  12. Tripathi, K.P., Evangelista, D., Zuccaro, A., Guarracino, M.R.: Transcriptator: An automated computational pipeline to annotate assembled reads and identify non coding RNA. PLoS ONE 10(11), e0140268 (2015)

    Article  Google Scholar 

  13. Huang, D.W., et al.: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009)

    Article  Google Scholar 

  14. Binns, D., et al.: QuickGO: A web-based tool for gene ontology searching. Bioinformatics 25(22), 3045–3046 (2009)

    Article  Google Scholar 

  15. Huang, D.W., Sherman, B.T., Lempicki, R.A.: Bioinformatics enrichment tools: toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37(1), 1–13 (2009)

    Article  Google Scholar 

  16. Piovesan, D., et al.: How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinformatics 14(Suppl 3), S4 (2013)

    Google Scholar 

  17. Galperin, M.Y., Makarova, K.S., Wolf, Y.I., Koonin, E.V.: Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43(D1), D261–D269 (2015)

    Article  Google Scholar 

  18. Mitchell, L., et al.: The interpro protein families database: the classification resource after 15 years. Nucleic Acids Res. Database Issue 43, D213–D221 (2015)

    Article  Google Scholar 

  19. Finn, R.D., et al.: The Pfam protein families database. Nucleic Acids Res. Database Issue 42, D222–D230 (2014)

    Article  Google Scholar 

  20. Letunic, I., Doerks, T., Bork, P.: SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 43, D257–D260 (2014). doi:10.1093/nar/gku949

    Article  Google Scholar 

  21. Kanehisa, M., Goto, S.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30 (2000)

    Article  Google Scholar 

  22. Becker, K.G., White, S.L., Muller, J., Engel, J.: BBID: The biological biochemical image database. Bioinformatics 16(8), 745–746 (2000)

    Article  Google Scholar 

  23. Thomas, P.D., et al.: PANTHER: A library of protein families and subfamilies indexed by function. Genome Res. 13, 2129–2141 (2003)

    Article  Google Scholar 

  24. The Apache HTTP Server Project. https://httpd.apache.org

  25. The World’s Most Popular Open Source Database. https://www.mysql.com

  26. phpMyAdmin to Handle the Administration of MySQL over the Web. http://www.phpmyadmin.net

  27. A Popular General-purpose Scripting Language that Is Especially Suited to Web Development. http://php.net

  28. The Lightweight, Interpreted, Object-oriented Scripting Language for Web Pages. http://www.ecma-international.org

  29. HTML: The Markup Language for Describing Web Documents. http://www.w3.org/TR/html5

  30. Cascading Style Sheets: a Mechanism for Adding Style to Web Documents. http://www.w3.org/Style/CSS

  31. Shumaker, R.W., Beck, B.B.: Primates in Question. Smithsonian Institution Press, Washington, DC (2003)

    Google Scholar 

  32. Worley, K.C., et al.: The common marmoset genome provides insight into primate biology and evolution. Nat. Genet. 46(8), 850–857 (2014)

    Article  Google Scholar 

  33. Romero, I.G., Ruvinsky, I., Gilad, Y.: Comparative studies of gene expression and the evolution of gene regulation. Nat. Rev. Genet. 13(7), 505–516 (2012)

    Article  Google Scholar 

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Acknowledgments

This work was funded by INTEROMICS flagship Italian project, PON02-00612-3461281 and PON02-00619-3470457. Mario R. Guarracino work has been conducted at National Research University Higher School of Economics and supported by RSF grant 14-41-00039.

The research group would like to thank Giuseppe Trerotola (ICAR/CNR) for technical support.

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Authors and Affiliations

  1. Laboratory for Genomics, Transcriptomics and Proteomics (LAB-GTP), High Performance Computing and Networking Institute (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131, Naples, Italy

    Daniela Evangelista, Mariano Avino, Kumar Parijat Tripathi & Mario Rosario Guarracino

Authors
  1. Daniela Evangelista
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  2. Mariano Avino
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  3. Kumar Parijat Tripathi
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  4. Mario Rosario Guarracino
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Corresponding author

Correspondence to Daniela Evangelista .

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Editors and Affiliations

  1. CNR, Istituto per le Applicazioni del Calcolo, Naples, Italy

    Claudia Angelini

  2. Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milano, Italy

    Paola MV Rancoita

  3. DIBRIS, University of Genoa, Genova, Italy

    Stefano Rovetta

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Evangelista, D., Avino, M., Tripathi, K.P., Guarracino, M.R. (2016). A Web Resource on Skeletal Muscle Transcriptome of Primates. In: Angelini, C., Rancoita, P., Rovetta, S. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2015. Lecture Notes in Computer Science(), vol 9874. Springer, Cham. https://doi.org/10.1007/978-3-319-44332-4_21

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  • DOI: https://doi.org/10.1007/978-3-319-44332-4_21

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-44331-7

  • Online ISBN: 978-3-319-44332-4

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