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Signaling pathways activation profiles make better markers of cancer than expression of individual genes
Identification of reliable and accurate molecular markers remains one of the major challenges of contemporary biomedicine. We developed a new bioinformatic technique termed OncoFinder that for the first time enables to quantatively measure activation of intracellular signaling pathways basing on tra...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Impact Journals LLC
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259415/ https://www.ncbi.nlm.nih.gov/pubmed/25415353 |
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author | Borisov, Nikolay M. Terekhanova, Nadezhda V. Aliper, Alexander M. Venkova, Larisa S. Smirnov, Philip Yu Roumiantsev, Sergey Korzinkin, Mikhail B. Zhavoronkov, Alex A. Buzdin, Anton A. |
author_facet | Borisov, Nikolay M. Terekhanova, Nadezhda V. Aliper, Alexander M. Venkova, Larisa S. Smirnov, Philip Yu Roumiantsev, Sergey Korzinkin, Mikhail B. Zhavoronkov, Alex A. Buzdin, Anton A. |
author_sort | Borisov, Nikolay M. |
collection | PubMed |
description | Identification of reliable and accurate molecular markers remains one of the major challenges of contemporary biomedicine. We developed a new bioinformatic technique termed OncoFinder that for the first time enables to quantatively measure activation of intracellular signaling pathways basing on transcriptomic data. Signaling pathways regulate all major cellular events in health and disease. Here, we showed that the Pathway Activation Strength (PAS) value itself may serve as the biomarker for cancer, and compared it with the “traditional” molecular markers based on the expression of individual genes. We applied OncoFinder to profile gene expression datasets for the nine human cancer types including bladder cancer, basal cell carcinoma, glioblastoma, hepatocellular carcinoma, lung adenocarcinoma, oral tongue squamous cell carcinoma, primary melanoma, prostate cancer and renal cancer, totally 292 cancer and 128 normal tissue samples taken from the Gene expression omnibus (GEO) repository. We profiled activation of 82 signaling pathways that involve ~2700 gene products. For 9/9 of the cancer types tested, the PAS values showed better area-under-the-curve (AUC) scores compared to the individual genes enclosing each of the pathways. These results evidence that the PAS values can be used as a new type of cancer biomarkers, superior to the traditional gene expression biomarkers. |
format | Online Article Text |
id | pubmed-4259415 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Impact Journals LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-42594152014-12-10 Signaling pathways activation profiles make better markers of cancer than expression of individual genes Borisov, Nikolay M. Terekhanova, Nadezhda V. Aliper, Alexander M. Venkova, Larisa S. Smirnov, Philip Yu Roumiantsev, Sergey Korzinkin, Mikhail B. Zhavoronkov, Alex A. Buzdin, Anton A. Oncotarget Research Paper Identification of reliable and accurate molecular markers remains one of the major challenges of contemporary biomedicine. We developed a new bioinformatic technique termed OncoFinder that for the first time enables to quantatively measure activation of intracellular signaling pathways basing on transcriptomic data. Signaling pathways regulate all major cellular events in health and disease. Here, we showed that the Pathway Activation Strength (PAS) value itself may serve as the biomarker for cancer, and compared it with the “traditional” molecular markers based on the expression of individual genes. We applied OncoFinder to profile gene expression datasets for the nine human cancer types including bladder cancer, basal cell carcinoma, glioblastoma, hepatocellular carcinoma, lung adenocarcinoma, oral tongue squamous cell carcinoma, primary melanoma, prostate cancer and renal cancer, totally 292 cancer and 128 normal tissue samples taken from the Gene expression omnibus (GEO) repository. We profiled activation of 82 signaling pathways that involve ~2700 gene products. For 9/9 of the cancer types tested, the PAS values showed better area-under-the-curve (AUC) scores compared to the individual genes enclosing each of the pathways. These results evidence that the PAS values can be used as a new type of cancer biomarkers, superior to the traditional gene expression biomarkers. Impact Journals LLC 2014-08-23 /pmc/articles/PMC4259415/ /pubmed/25415353 Text en Copyright: © 2014 Borisov et al. http://creativecommons.org/licenses/by/2.5/ 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 credited |
spellingShingle | Research Paper Borisov, Nikolay M. Terekhanova, Nadezhda V. Aliper, Alexander M. Venkova, Larisa S. Smirnov, Philip Yu Roumiantsev, Sergey Korzinkin, Mikhail B. Zhavoronkov, Alex A. Buzdin, Anton A. Signaling pathways activation profiles make better markers of cancer than expression of individual genes |
title | Signaling pathways activation profiles make better markers of cancer than expression of individual genes |
title_full | Signaling pathways activation profiles make better markers of cancer than expression of individual genes |
title_fullStr | Signaling pathways activation profiles make better markers of cancer than expression of individual genes |
title_full_unstemmed | Signaling pathways activation profiles make better markers of cancer than expression of individual genes |
title_short | Signaling pathways activation profiles make better markers of cancer than expression of individual genes |
title_sort | signaling pathways activation profiles make better markers of cancer than expression of individual genes |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259415/ https://www.ncbi.nlm.nih.gov/pubmed/25415353 |
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