Literature DB >> 21063957

Identification of alternatively spliced transcripts using a proteomic informatics approach.

Rajasree Menon1, Gilbert S Omenn.   

Abstract

We present the protocol for the identification of alternatively spliced peptide sequences from tandem mass spectrometry datasets searched using X!Tandem against our modified ECgene resource with all potential translation products and then matched with the Michigan Peptide to Protein Integration (MPPI) scheme. This approach is suitable for human and mouse datasets. Application of the method is illustrated with a study of the Kras activation-Ink4/Arf deletion mouse model of human pancreatic ductal adenocarcinoma.

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Year:  2011        PMID： 21063957      PMCID： PMC4123872          DOI： 10.1007/978-1-60761-987-1_20

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  14 in total

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Authors:  D K Han; J Eng; H Zhou; R Aebersold
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Review 3.  Pre-mRNA splicing and human disease.

Authors:  Nuno André Faustino; Thomas A Cooper
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Review 4.  The relevance of alternative RNA splicing to pharmacogenomics.

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5.  BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Authors:  Scott McGinnis; Thomas L Madden
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

6.  TANDEM: matching proteins with tandem mass spectra.

Authors:  Robertson Craig; Ronald C Beavis
Journal:  Bioinformatics       Date:  2004-02-19       Impact factor: 6.937

7.  ECgene: genome-based EST clustering and gene modeling for alternative splicing.

Authors:  Namshin Kim; Seokmin Shin; Sanghyuk Lee
Journal:  Genome Res       Date:  2005-04       Impact factor: 9.043

Review 8.  Aberrant and alternative splicing in cancer.

Authors:  Julian P Venables
Journal:  Cancer Res       Date:  2004-11-01       Impact factor: 12.701

9.  Alternative splicing in disease and therapy.

Authors:  Mariano A Garcia-Blanco; Andrew P Baraniak; Erika L Lasda
Journal:  Nat Biotechnol       Date:  2004-05       Impact factor: 54.908

10.  InterProScan: protein domains identifier.

Authors:  E Quevillon; V Silventoinen; S Pillai; N Harte; N Mulder; R Apweiler; R Lopez
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Authors:  Pratik Jagtap; Jill Goslinga; Joel A Kooren; Thomas McGowan; Matthew S Wroblewski; Sean L Seymour; Timothy J Griffin
Journal:  Proteomics       Date:  2013-03-15       Impact factor: 3.984

5.  Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.

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Journal:  PLoS Comput Biol       Date:  2013-11-07       Impact factor: 4.475

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Review 7.  Oncogenic alternative splicing switches: role in cancer progression and prospects for therapy.

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Journal:  Int J Cell Biol       Date:  2013-10-27
  7 in total

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