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Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis
Cancer is recognized to be a family of gene-based diseases whose causes are to be found in disruptions of basic biologic processes. An increasingly deep catalogue of canonical networks details the specific molecular interaction of genes and their products. However, mapping of disease phenotypes to a...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855990/ https://www.ncbi.nlm.nih.gov/pubmed/17487280 http://dx.doi.org/10.1371/journal.pone.0000425 |
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author | Efroni, Sol Schaefer, Carl F. Buetow, Kenneth H. |
author_facet | Efroni, Sol Schaefer, Carl F. Buetow, Kenneth H. |
author_sort | Efroni, Sol |
collection | PubMed |
description | Cancer is recognized to be a family of gene-based diseases whose causes are to be found in disruptions of basic biologic processes. An increasingly deep catalogue of canonical networks details the specific molecular interaction of genes and their products. However, mapping of disease phenotypes to alterations of these networks of interactions is accomplished indirectly and non-systematically. Here we objectively identify pathways associated with malignancy, staging, and outcome in cancer through application of an analytic approach that systematically evaluates differences in the activity and consistency of interactions within canonical biologic processes. Using large collections of publicly accessible genome-wide gene expression, we identify small, common sets of pathways – Trka Receptor, Apoptosis response to DNA Damage, Ceramide, Telomerase, CD40L and Calcineurin – whose differences robustly distinguish diverse tumor types from corresponding normal samples, predict tumor grade, and distinguish phenotypes such as estrogen receptor status and p53 mutation state. Pathways identified through this analysis perform as well or better than phenotypes used in the original studies in predicting cancer outcome. This approach provides a means to use genome-wide characterizations to map key biological processes to important clinical features in disease. |
format | Text |
id | pubmed-1855990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-18559902007-05-09 Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis Efroni, Sol Schaefer, Carl F. Buetow, Kenneth H. PLoS One Research Article Cancer is recognized to be a family of gene-based diseases whose causes are to be found in disruptions of basic biologic processes. An increasingly deep catalogue of canonical networks details the specific molecular interaction of genes and their products. However, mapping of disease phenotypes to alterations of these networks of interactions is accomplished indirectly and non-systematically. Here we objectively identify pathways associated with malignancy, staging, and outcome in cancer through application of an analytic approach that systematically evaluates differences in the activity and consistency of interactions within canonical biologic processes. Using large collections of publicly accessible genome-wide gene expression, we identify small, common sets of pathways – Trka Receptor, Apoptosis response to DNA Damage, Ceramide, Telomerase, CD40L and Calcineurin – whose differences robustly distinguish diverse tumor types from corresponding normal samples, predict tumor grade, and distinguish phenotypes such as estrogen receptor status and p53 mutation state. Pathways identified through this analysis perform as well or better than phenotypes used in the original studies in predicting cancer outcome. This approach provides a means to use genome-wide characterizations to map key biological processes to important clinical features in disease. Public Library of Science 2007-05-09 /pmc/articles/PMC1855990/ /pubmed/17487280 http://dx.doi.org/10.1371/journal.pone.0000425 Text en This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. |
spellingShingle | Research Article Efroni, Sol Schaefer, Carl F. Buetow, Kenneth H. Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis |
title | Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis |
title_full | Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis |
title_fullStr | Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis |
title_full_unstemmed | Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis |
title_short | Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis |
title_sort | identification of key processes underlying cancer phenotypes using biologic pathway analysis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855990/ https://www.ncbi.nlm.nih.gov/pubmed/17487280 http://dx.doi.org/10.1371/journal.pone.0000425 |
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