Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
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Date
2016-06-02Author
Wright, JC
Mudge, J
Weisser, H
Barzine, MP
Gonzalez, JM
Brazma, A
Choudhary, JS
Harrow, J
Type
Journal Article
Metadata
Show full item recordAbstract
Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing field of proteogenomics provides evidence for the translation of genes into proteins and can be used to discover and refine gene models. However, for both the proteomics and annotation groups, there is a lack of guidelines for integrating this data. Here we report a stringent workflow for the interpretation of proteogenomic data that could be used by the annotation community to interpret novel proteogenomic evidence. Based on reprocessing of three large-scale publicly available human data sets, we show that a conservative approach, using stringent filtering is required to generate valid identifications. Evidence has been found supporting 16 novel protein-coding genes being added to GENCODE. Despite this many peptide identifications in pseudogenes cannot be annotated due to the absence of orthogonal supporting evidence.
Collections
Subject
Humans
Proteins
Gene Expression Regulation
Amino Acid Sequence
Open Reading Frames
Pseudogenes
Genome, Human
Molecular Sequence Annotation
Gene Ontology
Proteogenomics
Research team
Functional Proteomics Group
Language
eng
Date accepted
2016-04-28
License start date
2016-06-02
Citation
Nature communications, 2016, 7 pp. 11778 - ?
Publisher
NATURE PORTFOLIO