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Atlas of Signaling for Interpretation of Microarray Experiments

Microarray-based expression profiling of living systems is a quick and inexpensive method to obtain insights into the nature of various diseases and phenotypes. A typical microarray profile can yield hundreds or even thousands of differentially expressed genes and finding biologically plausible them...

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Detalles Bibliográficos
Autores principales: Kotelnikova, Ekaterina, Ivanikova, Natalia, Kalinin, Andrey, Yuryev, Anton, Daraselia, Nikolai
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822851/
https://www.ncbi.nlm.nih.gov/pubmed/20174649
http://dx.doi.org/10.1371/journal.pone.0009256
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author Kotelnikova, Ekaterina
Ivanikova, Natalia
Kalinin, Andrey
Yuryev, Anton
Daraselia, Nikolai
author_facet Kotelnikova, Ekaterina
Ivanikova, Natalia
Kalinin, Andrey
Yuryev, Anton
Daraselia, Nikolai
author_sort Kotelnikova, Ekaterina
collection PubMed
description Microarray-based expression profiling of living systems is a quick and inexpensive method to obtain insights into the nature of various diseases and phenotypes. A typical microarray profile can yield hundreds or even thousands of differentially expressed genes and finding biologically plausible themes or regulatory mechanisms underlying these changes is a non-trivial and daunting task. We describe a novel approach for systems-level interpretation of microarray expression data using a manually constructed “overview” pathway depicting the main cellular signaling channels (Atlas of Signaling). Currently, the developed pathway focuses on signal transduction from surface receptors to transcription factors and further transcriptional regulation of cellular “workhorse” proteins. We show how the constructed Atlas of Signaling in combination with an enrichment analysis algorithm allows quick identification and visualization of the main signaling cascades and cellular processes affected in a gene expression profiling experiment. We validate our approach using several publicly available gene expression datasets.
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spelling pubmed-28228512010-02-20 Atlas of Signaling for Interpretation of Microarray Experiments Kotelnikova, Ekaterina Ivanikova, Natalia Kalinin, Andrey Yuryev, Anton Daraselia, Nikolai PLoS One Research Article Microarray-based expression profiling of living systems is a quick and inexpensive method to obtain insights into the nature of various diseases and phenotypes. A typical microarray profile can yield hundreds or even thousands of differentially expressed genes and finding biologically plausible themes or regulatory mechanisms underlying these changes is a non-trivial and daunting task. We describe a novel approach for systems-level interpretation of microarray expression data using a manually constructed “overview” pathway depicting the main cellular signaling channels (Atlas of Signaling). Currently, the developed pathway focuses on signal transduction from surface receptors to transcription factors and further transcriptional regulation of cellular “workhorse” proteins. We show how the constructed Atlas of Signaling in combination with an enrichment analysis algorithm allows quick identification and visualization of the main signaling cascades and cellular processes affected in a gene expression profiling experiment. We validate our approach using several publicly available gene expression datasets. Public Library of Science 2010-02-17 /pmc/articles/PMC2822851/ /pubmed/20174649 http://dx.doi.org/10.1371/journal.pone.0009256 Text en Kotelnikova et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Kotelnikova, Ekaterina
Ivanikova, Natalia
Kalinin, Andrey
Yuryev, Anton
Daraselia, Nikolai
Atlas of Signaling for Interpretation of Microarray Experiments
title Atlas of Signaling for Interpretation of Microarray Experiments
title_full Atlas of Signaling for Interpretation of Microarray Experiments
title_fullStr Atlas of Signaling for Interpretation of Microarray Experiments
title_full_unstemmed Atlas of Signaling for Interpretation of Microarray Experiments
title_short Atlas of Signaling for Interpretation of Microarray Experiments
title_sort atlas of signaling for interpretation of microarray experiments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822851/
https://www.ncbi.nlm.nih.gov/pubmed/20174649
http://dx.doi.org/10.1371/journal.pone.0009256
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