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ASPicDB: A Database Web Tool for Alternative Splicing Analysis

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RNA Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1269))

Abstract

Alternative splicing (AS) is a basic molecular phenomenon that increases the functional complexity of higher eukaryotic transcriptomes. Indeed, through AS individual gene loci can generate multiple RNAs from the same pre-mRNA. AS has been investigated in a variety of clinical and pathological studies, such as the transcriptome regulation in cancer. In human, recent works based on massive RNA sequencing indicate that >95 % of pre-mRNAs are processed to yield multiple transcripts. Given the biological relevance of AS, several computational efforts have been done leading to the implementation of novel algorithms and specific specialized databases. Here we describe the web application ASPicDB that allows the recovery of detailed biological information about the splicing mechanism. ASPicDB provides powerful querying systems to interrogate AS events at gene, transcript, and protein levels. Finally, ASPicDB includes web visualization instruments to browse and export results for further off-line analyses.

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References

  1. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40(12):1413–1415

    Article  CAS  PubMed  Google Scholar 

  3. Hallegger M, Llorian M, Smith CW (2010) Alternative splicing: global insights. FEBS J 277(4):856–866

    Article  CAS  PubMed  Google Scholar 

  4. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ (2010) Deciphering the splicing code. Nature 465:53–59

    Article  CAS  PubMed  Google Scholar 

  5. Castrignanò T, D’Antonio M, Anselmo A, Carrabino D, D’Onorio De Meo A, D'Erchia AM, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G (2008) ASPicDB: a database resource for alternative splicing analysis. Bioinformatics 24(10):1300–1304

    Article  PubMed  Google Scholar 

  6. Martelli PL, D’Antonio M, Bonizzoni P, Castrignanò T, D’Erchia AM, D’Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole G (2011) ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res 39(Database issue):D80–D85

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  8. Bonizzoni P, Rizzi R, Pesole G (2005) ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics 6:244

    Article  PubMed Central  PubMed  Google Scholar 

  9. Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P (2012) PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. BMC Bioinformatics 13(Suppl 5):S2. doi:10.1186/1471-2105-13-S5-S2

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Pontius JU, Wagner L, Schuler GD (2003) UniGene: a unified view of the transcriptome. In: McEntyre J, Ostell J The NCBI Handbook. Bethesda, MD: National Center for Biotechnology Information

    Google Scholar 

  11. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) Genbank. Nucleic Acids Res 41(Database issue):D36–D42

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. refseq. http://www.ncbi.nlm.nih.gov/pubmed/24259432

  13. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A (2007) UniProtKB/Swiss-Prot. Methods Mol Biol 406:89–112

    CAS  PubMed  Google Scholar 

  14. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235–242

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Pfam database. ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/

  16. Uniref 90. http://www.uniprot.org/help/uniref

  17. Giulietti M, Piva F, D’Antonio M, D’Onorio De Meo P, Paoletti D, Castrignanò T, D’Erchia AM, Picardi E, Zambelli F, Principato G, Pavesi G, Pesole G (2013) SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res 41(Database issue):D125–D131

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  19. Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA (2013) Genenames.org: the HGNC resources in 2013. Nucleic Acids Res 41(Database issue):D545–D552. doi:10.1093/nar/gks1066, Epub 2012 Nov 17

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 33(Database issue):D54–D58

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33(Database issue):D514–D517

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Riva A, Pesole G (2009) A unique, consistent identifier for alternatively spliced transcript variants. PLoS One 4(10):e7631

    Article  PubMed Central  PubMed  Google Scholar 

  24. Zhang H, Hu J, Recce M, Tian B (2005) PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res 33(Database issue):D116–D120

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Kim N, Alekseyenko AV, Roy M, Lee C (2007) The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res 35(Database issue):D93–D98

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 34:D46–D55

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Thierry-Mieg D, Thierry-Mieg J (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol 7 (Suppl 1), S12, 1–14

    Google Scholar 

  28. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R (2006) The PeptideAtlas project. Nucleic Acids Res 34(Database issue):D655–D658

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  29. Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y (2006) CAGE basic/analysis databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res 34(Database issue):D632–D636

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M (2002) The Ensembl genome database project. Nucleic Acids Res 30(1):38–41

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Pierleoni A, Martelli PL, Fariselli P, Casadio R (2006) BaCelLo: a balanced subcellular localization predictor. Bioinformatics 22(14):e408–e416

    Article  CAS  PubMed  Google Scholar 

  32. Fariselli P, Finocchiaro G, Casadio R (2003) SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19(18):2498–2499

    Article  CAS  PubMed  Google Scholar 

  33. Pierleoni A, Martelli PL, Casadio R (2008) PredGPI: a GPI-anchor predictor. BMC Bioinformatics 9:392–395. doi:10.1186/1471-2105-9-392

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the Italian Ministero dell’Istruzione, Università e Ricerca (MIUR): PRIN 2009 and 2010 and Consiglio Nazionale delle Ricerche: Flagship Project Epigen, Medicina Personalizzata and Aging Program 2012–2014.

Author information

Authors and Affiliations

  1. Consorzio Interuniversitario CINECA, 00185, Rome, Italy

    Mattia D’Antonio & Tiziana Castrgnanò

  2. Translational Oncogenomics Unit, Italian National Cancer Institute “Regina Elena”, Rome, Italy

    Matteo Pallocca

  3. Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126, Bari, Italy

    Anna Maria D’Erchia, Ernesto Picardi & Graziano Pesole

  4. Institute of Biomembranes and Bioenergetics, National Research Council, 70126, Bari, Italy

    Anna Maria D’Erchia, Ernesto Picardi & Graziano Pesole

  5. National Institute of Biostructures and Biosystems (INBB), 00136, Rome, Italy

    Ernesto Picardi & Graziano Pesole

Authors
  1. Mattia D’Antonio
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  2. Tiziana Castrgnanò
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  3. Matteo Pallocca
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  4. Anna Maria D’Erchia
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  5. Ernesto Picardi
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  6. Graziano Pesole
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Corresponding author

Correspondence to Graziano Pesole .

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Editors and Affiliations

  1. Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research Council, University of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB), Rome, Italy

    Ernesto Picardi

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D’Antonio, M., Castrgnanò, T., Pallocca, M., D’Erchia, A.M., Picardi, E., Pesole, G. (2015). ASPicDB: A Database Web Tool for Alternative Splicing Analysis. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_23

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  • DOI: https://doi.org/10.1007/978-1-4939-2291-8_23

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2290-1

  • Online ISBN: 978-1-4939-2291-8

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