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Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer
To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415781/ https://www.ncbi.nlm.nih.gov/pubmed/25928635 http://dx.doi.org/10.1371/journal.pone.0125013 |
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author | Li, Hao Yu, Beiqin Li, Jianfang Su, Liping Yan, Min Zhang, Jun Li, Chen Zhu, Zhenggang Liu, Bingya |
author_facet | Li, Hao Yu, Beiqin Li, Jianfang Su, Liping Yan, Min Zhang, Jun Li, Chen Zhu, Zhenggang Liu, Bingya |
author_sort | Li, Hao |
collection | PubMed |
description | To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) value was < 0.01, P-value was <0.01 and the fold change (FC) was >2. Subsequently, Gene Ontology (GO) categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease. |
format | Online Article Text |
id | pubmed-4415781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-44157812015-05-07 Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer Li, Hao Yu, Beiqin Li, Jianfang Su, Liping Yan, Min Zhang, Jun Li, Chen Zhu, Zhenggang Liu, Bingya PLoS One Research Article To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) value was < 0.01, P-value was <0.01 and the fold change (FC) was >2. Subsequently, Gene Ontology (GO) categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease. Public Library of Science 2015-04-30 /pmc/articles/PMC4415781/ /pubmed/25928635 http://dx.doi.org/10.1371/journal.pone.0125013 Text en © 2015 Li 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 Li, Hao Yu, Beiqin Li, Jianfang Su, Liping Yan, Min Zhang, Jun Li, Chen Zhu, Zhenggang Liu, Bingya Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer |
title | Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer |
title_full | Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer |
title_fullStr | Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer |
title_full_unstemmed | Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer |
title_short | Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer |
title_sort | characterization of differentially expressed genes involved in pathways associated with gastric cancer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415781/ https://www.ncbi.nlm.nih.gov/pubmed/25928635 http://dx.doi.org/10.1371/journal.pone.0125013 |
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