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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...

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Autores principales: Li, Hao, Yu, Beiqin, Li, Jianfang, Su, Liping, Yan, Min, Zhang, Jun, Li, Chen, Zhu, Zhenggang, Liu, Bingya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
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.
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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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