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B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis
The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utiliz...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054497/ https://www.ncbi.nlm.nih.gov/pubmed/22917187 http://dx.doi.org/10.1016/j.gpb.2012.03.001 |
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author | Towfic, Fadi Gupta, Shakti Honavar, Vasant Subramaniam, Shankar |
author_facet | Towfic, Fadi Gupta, Shakti Honavar, Vasant Subramaniam, Shankar |
author_sort | Towfic, Fadi |
collection | PubMed |
description | The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands. First, we compared the degree distributions of the generated networks. Second, we utilized a pairwise network alignment algorithm, BiNA, to align the networks based on the hubs in the networks. Third, we aligned the networks based on a set of KEGG pathways. We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition. The resulting pathways were further validated through literature for their common physiological responses. Collectively, the results based on our comparative analyses of degree distributions, alignment of hubs, and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches (e.g., gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells. |
format | Online Article Text |
id | pubmed-5054497 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-50544972016-10-14 B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis Towfic, Fadi Gupta, Shakti Honavar, Vasant Subramaniam, Shankar Genomics Proteomics Bioinformatics Original Research The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands. First, we compared the degree distributions of the generated networks. Second, we utilized a pairwise network alignment algorithm, BiNA, to align the networks based on the hubs in the networks. Third, we aligned the networks based on a set of KEGG pathways. We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition. The resulting pathways were further validated through literature for their common physiological responses. Collectively, the results based on our comparative analyses of degree distributions, alignment of hubs, and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches (e.g., gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells. Elsevier 2012-06 2012-06-25 /pmc/articles/PMC5054497/ /pubmed/22917187 http://dx.doi.org/10.1016/j.gpb.2012.03.001 Text en © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Published by Elsevier Ltd and Science Press. All rights reserved. http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/). |
spellingShingle | Original Research Towfic, Fadi Gupta, Shakti Honavar, Vasant Subramaniam, Shankar B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis |
title | B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis |
title_full | B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis |
title_fullStr | B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis |
title_full_unstemmed | B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis |
title_short | B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis |
title_sort | b-cell ligand processing pathways detected by large-scale comparative analysis |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054497/ https://www.ncbi.nlm.nih.gov/pubmed/22917187 http://dx.doi.org/10.1016/j.gpb.2012.03.001 |
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