Identification of significant features by the Global Mean Rank test.

With the introduction of omics-technologies such as transcriptomics and proteomics, numerous methods for the reliable identification of significantly regulated features (genes, proteins, etc.) have been developed. Experimental practice requires these tests to successfully deal with conditions such a...

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Autores principales:	Martin Klammer, J Nikolaj Dybowski, Daniel Hoffmann, Christoph Schaab
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/68a9b404cbf947448e605a83457dba17
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spelling	oai:doaj.org-article:68a9b404cbf947448e605a83457dba172021-11-25T06:04:49ZIdentification of significant features by the Global Mean Rank test.1932-620310.1371/journal.pone.0104504https://doaj.org/article/68a9b404cbf947448e605a83457dba172014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25119995/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203With the introduction of omics-technologies such as transcriptomics and proteomics, numerous methods for the reliable identification of significantly regulated features (genes, proteins, etc.) have been developed. Experimental practice requires these tests to successfully deal with conditions such as small numbers of replicates, missing values, non-normally distributed expression levels, and non-identical distributions of features. With the MeanRank test we aimed at developing a test that performs robustly under these conditions, while favorably scaling with the number of replicates. The test proposed here is a global one-sample location test, which is based on the mean ranks across replicates, and internally estimates and controls the false discovery rate. Furthermore, missing data is accounted for without the need of imputation. In extensive simulations comparing MeanRank to other frequently used methods, we found that it performs well with small and large numbers of replicates, feature dependent variance between replicates, and variable regulation across features on simulation data and a recent two-color microarray spike-in dataset. The tests were then used to identify significant changes in the phosphoproteomes of cancer cells induced by the kinase inhibitors erlotinib and 3-MB-PP1 in two independently published mass spectrometry-based studies. MeanRank outperformed the other global rank-based methods applied in this study. Compared to the popular Significance Analysis of Microarrays and Linear Models for Microarray methods, MeanRank performed similar or better. Furthermore, MeanRank exhibits more consistent behavior regarding the degree of regulation and is robust against the choice of preprocessing methods. MeanRank does not require any imputation of missing values, is easy to understand, and yields results that are easy to interpret. The software implementing the algorithm is freely available for academic and commercial use.Martin KlammerJ Nikolaj DybowskiDaniel HoffmannChristoph SchaabPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e104504 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Martin Klammer J Nikolaj Dybowski Daniel Hoffmann Christoph Schaab Identification of significant features by the Global Mean Rank test.
description	With the introduction of omics-technologies such as transcriptomics and proteomics, numerous methods for the reliable identification of significantly regulated features (genes, proteins, etc.) have been developed. Experimental practice requires these tests to successfully deal with conditions such as small numbers of replicates, missing values, non-normally distributed expression levels, and non-identical distributions of features. With the MeanRank test we aimed at developing a test that performs robustly under these conditions, while favorably scaling with the number of replicates. The test proposed here is a global one-sample location test, which is based on the mean ranks across replicates, and internally estimates and controls the false discovery rate. Furthermore, missing data is accounted for without the need of imputation. In extensive simulations comparing MeanRank to other frequently used methods, we found that it performs well with small and large numbers of replicates, feature dependent variance between replicates, and variable regulation across features on simulation data and a recent two-color microarray spike-in dataset. The tests were then used to identify significant changes in the phosphoproteomes of cancer cells induced by the kinase inhibitors erlotinib and 3-MB-PP1 in two independently published mass spectrometry-based studies. MeanRank outperformed the other global rank-based methods applied in this study. Compared to the popular Significance Analysis of Microarrays and Linear Models for Microarray methods, MeanRank performed similar or better. Furthermore, MeanRank exhibits more consistent behavior regarding the degree of regulation and is robust against the choice of preprocessing methods. MeanRank does not require any imputation of missing values, is easy to understand, and yields results that are easy to interpret. The software implementing the algorithm is freely available for academic and commercial use.
format	article
author	Martin Klammer J Nikolaj Dybowski Daniel Hoffmann Christoph Schaab
author_facet	Martin Klammer J Nikolaj Dybowski Daniel Hoffmann Christoph Schaab
author_sort	Martin Klammer
title	Identification of significant features by the Global Mean Rank test.
title_short	Identification of significant features by the Global Mean Rank test.
title_full	Identification of significant features by the Global Mean Rank test.
title_fullStr	Identification of significant features by the Global Mean Rank test.
title_full_unstemmed	Identification of significant features by the Global Mean Rank test.
title_sort	identification of significant features by the global mean rank test.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/68a9b404cbf947448e605a83457dba17
work_keys_str_mv	AT martinklammer identificationofsignificantfeaturesbytheglobalmeanranktest AT jnikolajdybowski identificationofsignificantfeaturesbytheglobalmeanranktest AT danielhoffmann identificationofsignificantfeaturesbytheglobalmeanranktest AT christophschaab identificationofsignificantfeaturesbytheglobalmeanranktest
_version_	1718414226979028992

Identification of significant features by the Global Mean Rank test.

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