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dc.contributor.authorLonsdale, A
dc.contributor.authorDavis, MJ
dc.contributor.authorDoblin, MS
dc.contributor.authorBacic, A
dc.date.accessioned2021-02-05T01:31:57Z
dc.date.available2021-02-05T01:31:57Z
dc.date.issued2016-09-27
dc.identifier.citationLonsdale, A., Davis, M. J., Doblin, M. S. & Bacic, A. (2016). Better Than Nothing? Limitations of the Prediction Tool SecretomeP in the Search for Leaderless Secretory Proteins (LSPs) in Plants. FRONTIERS IN PLANT SCIENCE, 7 (September2016), https://doi.org/10.3389/fpls.2015.01451.
dc.identifier.issn1664-462X
dc.identifier.urihttp://hdl.handle.net/11343/260432
dc.description.abstractIn proteomic analyses of the plant secretome, the presence of putative leaderless secretory proteins (LSPs) is difficult to confirm due to the possibility of contamination from other sub-cellular compartments. In the absence of a plant-specific tool for predicting LSPs, the mammalian-trained SecretomeP has been applied to plant proteins in multiple studies to identify the most likely LSPs. This study investigates the effectiveness of using SecretomeP on plant proteins, identifies its limitations and provides a benchmark for its use. In the absence of experimentally verified LSPs we exploit the common-feature hypothesis behind SecretomeP and use known classically secreted proteins (CSPs) of plants as a proxy to evaluate its accuracy. We show that, contrary to the common-feature hypothesis, plant CSPs are a poor proxy for evaluating LSP detection due to variation in the SecretomeP prediction scores when the signal peptide (SP) is modified. Removing the SP region from CSPs and comparing the predictive performance against non-secretory proteins indicates that commonly used threshold scores of 0.5 and 0.6 result in false-positive rates in excess of 0.3 when applied to plants proteins. Setting the false-positive rate to 0.05, consistent with the original mammalian performance of SecretomeP, yields only a marginally higher true positive rate compared to false positives. Therefore the use of SecretomeP on plant proteins is not recommended. This study investigates the trade-offs of using SecretomeP on plant proteins and provides insights into predictive features for future development of plant-specific common-feature tools.
dc.languageEnglish
dc.publisherFRONTIERS MEDIA SA
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleBetter Than Nothing? Limitations of the Prediction Tool SecretomeP in the Search for Leaderless Secretory Proteins (LSPs) in Plants
dc.typeJournal Article
dc.identifier.doi10.3389/fpls.2015.01451
melbourne.affiliation.departmentSchool of BioSciences
melbourne.affiliation.departmentSchool of Biomedical Sciences
melbourne.affiliation.departmentMedical Biology (W.E.H.I.)
melbourne.affiliation.facultyScience
melbourne.affiliation.facultyMedicine, Dentistry & Health Sciences
melbourne.source.titleFrontiers in Plant Science
melbourne.source.volume7
melbourne.source.issueSeptember2016
dc.rights.licenseCC BY
melbourne.elementsid1104041
melbourne.contributor.authorDoblin, Monika
melbourne.contributor.authorBacic, Anthony
melbourne.contributor.authorDavis, Melissa
melbourne.contributor.authorLONSDALE, ANDREA
melbourne.contributor.authorLonsdale, Andrew
dc.identifier.eissn1664-462X
melbourne.accessrightsOpen Access


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