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Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast
Revealing the gene regulatory systems among DNA and proteins in living cells is one of the central aims of systems biology. In this study, I used Structural Equation Modeling (SEM) in combination with stepwise factor analysis to infer the protein-DNA interactions for gene expression control from onl...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Libertas Academica
2011
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236004/ https://www.ncbi.nlm.nih.gov/pubmed/22272062 http://dx.doi.org/10.4137/GRSB.S7569 |
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author | Aburatani, Sachiyo |
author_facet | Aburatani, Sachiyo |
author_sort | Aburatani, Sachiyo |
collection | PubMed |
description | Revealing the gene regulatory systems among DNA and proteins in living cells is one of the central aims of systems biology. In this study, I used Structural Equation Modeling (SEM) in combination with stepwise factor analysis to infer the protein-DNA interactions for gene expression control from only gene expression profiles, in the absence of protein information. I applied my approach to infer the causalities within the well-studied serial transcriptional regulation composed of GAL-related genes in yeast. This allowed me to reveal the hierarchy of serial transcriptional regulation, including previously unclear protein-DNA interactions. The validity of the constructed model was demonstrated by comparing the results with previous reports describing the regulation of the transcription factors. Furthermore, the model revealed combinatory regulation by Gal4p and Gal80p. In this study, the target genes were divided into three types: those regulated by one factor and those controlled by a combination of two factors. |
format | Online Article Text |
id | pubmed-3236004 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Libertas Academica |
record_format | MEDLINE/PubMed |
spelling | pubmed-32360042012-01-23 Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast Aburatani, Sachiyo Gene Regul Syst Bio Original Research Revealing the gene regulatory systems among DNA and proteins in living cells is one of the central aims of systems biology. In this study, I used Structural Equation Modeling (SEM) in combination with stepwise factor analysis to infer the protein-DNA interactions for gene expression control from only gene expression profiles, in the absence of protein information. I applied my approach to infer the causalities within the well-studied serial transcriptional regulation composed of GAL-related genes in yeast. This allowed me to reveal the hierarchy of serial transcriptional regulation, including previously unclear protein-DNA interactions. The validity of the constructed model was demonstrated by comparing the results with previous reports describing the regulation of the transcription factors. Furthermore, the model revealed combinatory regulation by Gal4p and Gal80p. In this study, the target genes were divided into three types: those regulated by one factor and those controlled by a combination of two factors. Libertas Academica 2011-11-10 /pmc/articles/PMC3236004/ /pubmed/22272062 http://dx.doi.org/10.4137/GRSB.S7569 Text en © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. |
spellingShingle | Original Research Aburatani, Sachiyo Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast |
title | Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast |
title_full | Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast |
title_fullStr | Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast |
title_full_unstemmed | Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast |
title_short | Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast |
title_sort | application of structure equation modeling for inferring a serial transcriptional regulation in yeast |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236004/ https://www.ncbi.nlm.nih.gov/pubmed/22272062 http://dx.doi.org/10.4137/GRSB.S7569 |
work_keys_str_mv | AT aburatanisachiyo applicationofstructureequationmodelingforinferringaserialtranscriptionalregulationinyeast |