Cargando…
Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method
Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene priori...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Scientific World Journal
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354662/ https://www.ncbi.nlm.nih.gov/pubmed/22654636 http://dx.doi.org/10.1100/2012/842727 |
_version_ | 1782233254533791744 |
---|---|
author | Arias, Carlos Roberto Yeh, Hsiang-Yuan Soo, Von-Wun |
author_facet | Arias, Carlos Roberto Yeh, Hsiang-Yuan Soo, Von-Wun |
author_sort | Arias, Carlos Roberto |
collection | PubMed |
description | Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF). The method is based on finding relevant interactions on protein interaction networks, then scoring the genes using shortest paths and topological analysis, integrating the results using a voting scheme and a biological boosting. We applied two experiments, one is prostate primary and normal samples and the other is prostate primary tumor with and without lymph nodes metastasis. We used 137 truly prostate cancer genes as benchmark. In the first experiment, GP-MIDAS-VXEF outperforms all the other state-of-the-art methods in the benchmark by retrieving the truest related genes from the candidate set in the top 50 scores found. We applied the same technique to infer the significant biomarkers in prostate cancer with lymph nodes metastasis which is not established well. |
format | Online Article Text |
id | pubmed-3354662 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | The Scientific World Journal |
record_format | MEDLINE/PubMed |
spelling | pubmed-33546622012-05-31 Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method Arias, Carlos Roberto Yeh, Hsiang-Yuan Soo, Von-Wun ScientificWorldJournal Research Article Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF). The method is based on finding relevant interactions on protein interaction networks, then scoring the genes using shortest paths and topological analysis, integrating the results using a voting scheme and a biological boosting. We applied two experiments, one is prostate primary and normal samples and the other is prostate primary tumor with and without lymph nodes metastasis. We used 137 truly prostate cancer genes as benchmark. In the first experiment, GP-MIDAS-VXEF outperforms all the other state-of-the-art methods in the benchmark by retrieving the truest related genes from the candidate set in the top 50 scores found. We applied the same technique to infer the significant biomarkers in prostate cancer with lymph nodes metastasis which is not established well. The Scientific World Journal 2012-05-02 /pmc/articles/PMC3354662/ /pubmed/22654636 http://dx.doi.org/10.1100/2012/842727 Text en Copyright © 2012 Carlos Roberto Arias et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Arias, Carlos Roberto Yeh, Hsiang-Yuan Soo, Von-Wun Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method |
title | Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method |
title_full | Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method |
title_fullStr | Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method |
title_full_unstemmed | Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method |
title_short | Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method |
title_sort | biomarker identification for prostate cancer and lymph node metastasis from microarray data and protein interaction network using gene prioritization method |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354662/ https://www.ncbi.nlm.nih.gov/pubmed/22654636 http://dx.doi.org/10.1100/2012/842727 |
work_keys_str_mv | AT ariascarlosroberto biomarkeridentificationforprostatecancerandlymphnodemetastasisfrommicroarraydataandproteininteractionnetworkusinggeneprioritizationmethod AT yehhsiangyuan biomarkeridentificationforprostatecancerandlymphnodemetastasisfrommicroarraydataandproteininteractionnetworkusinggeneprioritizationmethod AT soovonwun biomarkeridentificationforprostatecancerandlymphnodemetastasisfrommicroarraydataandproteininteractionnetworkusinggeneprioritizationmethod |