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Precision and recall estimates for two-hybrid screens

Motivation: Yeast two-hybrid screens are an important method to map pairwise protein interactions. This method can generate spurious interactions (false discoveries), and true interactions can be missed (false negatives). Previously, we reported a capture–recapture estimator for bait-specific precis...

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Detalles Bibliográficos
Autores principales: Huang, Hailiang, Bader, Joel S.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639075/
https://www.ncbi.nlm.nih.gov/pubmed/19091773
http://dx.doi.org/10.1093/bioinformatics/btn640
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author Huang, Hailiang
Bader, Joel S.
author_facet Huang, Hailiang
Bader, Joel S.
author_sort Huang, Hailiang
collection PubMed
description Motivation: Yeast two-hybrid screens are an important method to map pairwise protein interactions. This method can generate spurious interactions (false discoveries), and true interactions can be missed (false negatives). Previously, we reported a capture–recapture estimator for bait-specific precision and recall. Here, we present an improved method that better accounts for heterogeneity in bait-specific error rates. Result: For yeast, worm and fly screens, we estimate the overall false discovery rates (FDRs) to be 9.9%, 13.2% and 17.0% and the false negative rates (FNRs) to be 51%, 42% and 28%. Bait-specific FDRs and the estimated protein degrees are then used to identify protein categories that yield more (or fewer) false positive interactions and more (or fewer) interaction partners. While membrane proteins have been suggested to have elevated FDRs, the current analysis suggests that intrinsic membrane proteins may actually have reduced FDRs. Hydrophobicity is positively correlated with decreased error rates and fewer interaction partners. These methods will be useful for future two-hybrid screens, which could use ultra-high-throughput sequencing for deeper sampling of interacting bait–prey pairs. Availability: All software (C source) and datasets are available as supplemental files and at http://www.baderzone.org under the Lesser GPL v. 3 license. Contact: joel.bader@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-26390752009-02-25 Precision and recall estimates for two-hybrid screens Huang, Hailiang Bader, Joel S. Bioinformatics Original Papers Motivation: Yeast two-hybrid screens are an important method to map pairwise protein interactions. This method can generate spurious interactions (false discoveries), and true interactions can be missed (false negatives). Previously, we reported a capture–recapture estimator for bait-specific precision and recall. Here, we present an improved method that better accounts for heterogeneity in bait-specific error rates. Result: For yeast, worm and fly screens, we estimate the overall false discovery rates (FDRs) to be 9.9%, 13.2% and 17.0% and the false negative rates (FNRs) to be 51%, 42% and 28%. Bait-specific FDRs and the estimated protein degrees are then used to identify protein categories that yield more (or fewer) false positive interactions and more (or fewer) interaction partners. While membrane proteins have been suggested to have elevated FDRs, the current analysis suggests that intrinsic membrane proteins may actually have reduced FDRs. Hydrophobicity is positively correlated with decreased error rates and fewer interaction partners. These methods will be useful for future two-hybrid screens, which could use ultra-high-throughput sequencing for deeper sampling of interacting bait–prey pairs. Availability: All software (C source) and datasets are available as supplemental files and at http://www.baderzone.org under the Lesser GPL v. 3 license. Contact: joel.bader@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2009-02-01 2008-12-17 /pmc/articles/PMC2639075/ /pubmed/19091773 http://dx.doi.org/10.1093/bioinformatics/btn640 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Papers
Huang, Hailiang
Bader, Joel S.
Precision and recall estimates for two-hybrid screens
title Precision and recall estimates for two-hybrid screens
title_full Precision and recall estimates for two-hybrid screens
title_fullStr Precision and recall estimates for two-hybrid screens
title_full_unstemmed Precision and recall estimates for two-hybrid screens
title_short Precision and recall estimates for two-hybrid screens
title_sort precision and recall estimates for two-hybrid screens
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639075/
https://www.ncbi.nlm.nih.gov/pubmed/19091773
http://dx.doi.org/10.1093/bioinformatics/btn640
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