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Alternative splicing (AS) has been well-investigated at the trancriptome level by the application of RNA-seq technology. There is an ongoing debate on the biological importance of AS to proteome complexity. A toolkit for accurately identifying AS from proteome data is urgently needed. Here, we develop a software called PASS to comprehensively detect AS events for the proteomics mass spectrometry (MS) data. Moreover, PASS is well compatible with MS identification by the proteogenomics approach, which provides novel AS candidates for proteome identification. The workflow of PASS mainly contains 5 core steps: transcripts reconstruction from RNA-Seq data, novel protein sequence generation, MS data searching, proSAM file formatting and AS detection. Access to the program from either step is supported. PASS is successfully applied to proteome data of mouse hepatocytes and 407 AS events are firstly identified with proteomics MS evidences. PASS is expected to be widely used to identify AS events on proteome data and provide a deeper understanding of the proteome isoforms. The PASS software is freely available at https://github.com/wupengomics/PASS. This article is protected by copyright. All rights reserved.
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A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
An RNA splicing factor that also binds DNA. It is essential for pre-mRNA spicing in the formation of early SPLICEOSOMES and catalytic step II. It binds specifically to polypyrimidine tracts in INTRONS and is involved in the regulation of ALTERNATIVE SPLICING by SIGNAL TRANSDUCTION PATHWAYS.
A family of regulatory factors essential for constitutive and alternative splicing in RNA metabolism.
The identification of selected parameters in newborn infants by various tests, examinations, or other procedures. Screening may be performed by clinical or laboratory measures. A screening test is designed to sort out healthy neonates (INFANT, NEWBORN) from those not well, but the screening test is not intended as a diagnostic device, rather instead as epidemiologic.
A heterogeneous-nuclear ribonucleoprotein that has specificity for AU-rich elements found in the 3'-region of mRNA and may play a role in RNA stability. Several isoforms of hnRNP D protein have been found to occur due to alternative mRNA splicing (RNA SPLICING).
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
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Multiple Sclerosis MS
Multiple sclerosis (MS) is the most common disabling neurological condition affecting 100,000 young adults in the UK. The condition results from autoimmune damage to myelin, causing interference in nerve signaling. Symptoms experienced depend on the pa...