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...
Autores principales: | , , , , |
---|---|
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 |