Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Loading...
Embargo End Date
ICR Authors
Authors
Wright, JC
Mudge, J
Weisser, H
Barzine, MP
Gonzalez, JM
Brazma, A
Choudhary, JS
Harrow, J
Mudge, J
Weisser, H
Barzine, MP
Gonzalez, JM
Brazma, A
Choudhary, JS
Harrow, J
Document Type
Journal Article
Date
2016-06-02
Date Accepted
2016-04-28
Abstract
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.
Citation
Nature communications, 2016, 7 pp. 11778 - ?
Source Title
Publisher
NATURE PORTFOLIO
ISSN
2041-1723
eISSN
2041-1723
Collections
Research Team
Functional Proteomics Group