Cargando…

BlotIt—Optimal alignment of Western blot and qPCR experiments

Biological systems are frequently analyzed by means of mechanistic mathematical models. In order to infer model parameters and provide a useful model that can be employed for systems understanding and hypothesis testing, the model is often calibrated on quantitative, time-resolved data. To do so, it...

Descripción completa

Detalles Bibliográficos
Autores principales: Kemmer, Svenja, Bang, Severin, Rosenblatt, Marcus, Timmer, Jens, Kaschek, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365137/
https://www.ncbi.nlm.nih.gov/pubmed/35947551
http://dx.doi.org/10.1371/journal.pone.0264295
_version_ 1784765279052496896
author Kemmer, Svenja
Bang, Severin
Rosenblatt, Marcus
Timmer, Jens
Kaschek, Daniel
author_facet Kemmer, Svenja
Bang, Severin
Rosenblatt, Marcus
Timmer, Jens
Kaschek, Daniel
author_sort Kemmer, Svenja
collection PubMed
description Biological systems are frequently analyzed by means of mechanistic mathematical models. In order to infer model parameters and provide a useful model that can be employed for systems understanding and hypothesis testing, the model is often calibrated on quantitative, time-resolved data. To do so, it is typically important to compare experimental measurements over broad time ranges and various experimental conditions, e.g. perturbations of the biological system. However, most of the established experimental techniques such as Western blot, or quantitative real-time polymerase chain reaction only provide measurements on a relative scale, since different sample volumes, experimental adjustments or varying development times of a gel lead to systematic shifts in the data. In turn, the number of measurements corresponding to the same scale enabling comparability is limited. Here, we present a new flexible method to align measurement data that obeys different scaling factors and compare it to existing normalization approaches. We propose an alignment model to estimate these scaling factors and provide the possibility to adapt this model depending on the measurement technique of interest. In addition, an error model can be specified to adequately weight the different data points and obtain scaling-model based confidence intervals of the finally scaled data points. Our approach is applicable to all sorts of relative measurements and does not need a particular experimental condition that has been measured over all available scales. An implementation of the method is provided with the R package blotIt including refined ways of visualization.
format Online
Article
Text
id pubmed-9365137
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-93651372022-08-11 BlotIt—Optimal alignment of Western blot and qPCR experiments Kemmer, Svenja Bang, Severin Rosenblatt, Marcus Timmer, Jens Kaschek, Daniel PLoS One Research Article Biological systems are frequently analyzed by means of mechanistic mathematical models. In order to infer model parameters and provide a useful model that can be employed for systems understanding and hypothesis testing, the model is often calibrated on quantitative, time-resolved data. To do so, it is typically important to compare experimental measurements over broad time ranges and various experimental conditions, e.g. perturbations of the biological system. However, most of the established experimental techniques such as Western blot, or quantitative real-time polymerase chain reaction only provide measurements on a relative scale, since different sample volumes, experimental adjustments or varying development times of a gel lead to systematic shifts in the data. In turn, the number of measurements corresponding to the same scale enabling comparability is limited. Here, we present a new flexible method to align measurement data that obeys different scaling factors and compare it to existing normalization approaches. We propose an alignment model to estimate these scaling factors and provide the possibility to adapt this model depending on the measurement technique of interest. In addition, an error model can be specified to adequately weight the different data points and obtain scaling-model based confidence intervals of the finally scaled data points. Our approach is applicable to all sorts of relative measurements and does not need a particular experimental condition that has been measured over all available scales. An implementation of the method is provided with the R package blotIt including refined ways of visualization. Public Library of Science 2022-08-10 /pmc/articles/PMC9365137/ /pubmed/35947551 http://dx.doi.org/10.1371/journal.pone.0264295 Text en © 2022 Kemmer et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kemmer, Svenja
Bang, Severin
Rosenblatt, Marcus
Timmer, Jens
Kaschek, Daniel
BlotIt—Optimal alignment of Western blot and qPCR experiments
title BlotIt—Optimal alignment of Western blot and qPCR experiments
title_full BlotIt—Optimal alignment of Western blot and qPCR experiments
title_fullStr BlotIt—Optimal alignment of Western blot and qPCR experiments
title_full_unstemmed BlotIt—Optimal alignment of Western blot and qPCR experiments
title_short BlotIt—Optimal alignment of Western blot and qPCR experiments
title_sort blotit—optimal alignment of western blot and qpcr experiments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9365137/
https://www.ncbi.nlm.nih.gov/pubmed/35947551
http://dx.doi.org/10.1371/journal.pone.0264295
work_keys_str_mv AT kemmersvenja blotitoptimalalignmentofwesternblotandqpcrexperiments
AT bangseverin blotitoptimalalignmentofwesternblotandqpcrexperiments
AT rosenblattmarcus blotitoptimalalignmentofwesternblotandqpcrexperiments
AT timmerjens blotitoptimalalignmentofwesternblotandqpcrexperiments
AT kaschekdaniel blotitoptimalalignmentofwesternblotandqpcrexperiments