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G9A performs important roles in the progression of breast cancer through upregulating its targets
Breast cancer (BC) is the most common type of malignancy in females worldwide, however, its underlying mechanisms remain poorly understood. The present study aimed to investigate the mechanisms behind the development and progression of BC and identify potential biomarkers for it. The chromatin immun...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
D.A. Spandidos
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453034/ https://www.ncbi.nlm.nih.gov/pubmed/28599414 http://dx.doi.org/10.3892/ol.2017.5977 |
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author | Jiang, Wenhua Liu, Pengfei Li, Xiaodong |
author_facet | Jiang, Wenhua Liu, Pengfei Li, Xiaodong |
author_sort | Jiang, Wenhua |
collection | PubMed |
description | Breast cancer (BC) is the most common type of malignancy in females worldwide, however, its underlying mechanisms remain poorly understood. The present study aimed to investigate the mechanisms behind the development and progression of BC and identify potential biomarkers for it. The chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) dataset GSM1642516 and gene expression dataset GSE34925 were downloaded from the Gene Expression Omnibus database. Affy and oligo packages were used for the background correction and normalization of the gene expression dataset. Based on Limma package and the criteria of a fold change >1.41 or <0.71, and a false discovery rate adjusted P-value <0.05, differentially-expressed genes (DEGs) in euchromatic histone lysine methyltransferase 2 (G9A) -knockout (KO) breast samples compared with control samples were identified. The Database for Annotation, Visualization and Integrated Analysis was used for the functional enrichment analysis of the DEGs. Bowtie 2 and model-based analysis of ChIP-Seq version 14 (macs14) were used for the mapping of raw reads and the identification of G9A binding sites (peaks), respectively. In addition, overlapping genes between the DEGs and genes in the peaks located in −3000 to 3000 bp centered in the transcription start sites (conpeaks) were screened out and microRNAs (miRNAs) believed to regulate those overlaps were identified through the TargetScan database. A total of 217 DEGs were identified in G9A-KO samples, which were mainly involved in the biological processes and pathways associated with the inflammatory response and cancer progression. A total of 10,422 peaks, containing 1,210 conpeaks involving 1,138 genes, were identified. Among the 1,138 genes, 15 were overlapped with the DEGs, and 35 miRNAs were identified to regulate those overlaps. Insulin-induced gene 1 was regulated by 9 genes in the miRNA-gene regulation network, which may indicate its importance in the progression of BC. The present study identified potential biomarkers of BC that may be useful in the diagnosis and treatment of patients with the disease. |
format | Online Article Text |
id | pubmed-5453034 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | D.A. Spandidos |
record_format | MEDLINE/PubMed |
spelling | pubmed-54530342017-06-08 G9A performs important roles in the progression of breast cancer through upregulating its targets Jiang, Wenhua Liu, Pengfei Li, Xiaodong Oncol Lett Articles Breast cancer (BC) is the most common type of malignancy in females worldwide, however, its underlying mechanisms remain poorly understood. The present study aimed to investigate the mechanisms behind the development and progression of BC and identify potential biomarkers for it. The chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) dataset GSM1642516 and gene expression dataset GSE34925 were downloaded from the Gene Expression Omnibus database. Affy and oligo packages were used for the background correction and normalization of the gene expression dataset. Based on Limma package and the criteria of a fold change >1.41 or <0.71, and a false discovery rate adjusted P-value <0.05, differentially-expressed genes (DEGs) in euchromatic histone lysine methyltransferase 2 (G9A) -knockout (KO) breast samples compared with control samples were identified. The Database for Annotation, Visualization and Integrated Analysis was used for the functional enrichment analysis of the DEGs. Bowtie 2 and model-based analysis of ChIP-Seq version 14 (macs14) were used for the mapping of raw reads and the identification of G9A binding sites (peaks), respectively. In addition, overlapping genes between the DEGs and genes in the peaks located in −3000 to 3000 bp centered in the transcription start sites (conpeaks) were screened out and microRNAs (miRNAs) believed to regulate those overlaps were identified through the TargetScan database. A total of 217 DEGs were identified in G9A-KO samples, which were mainly involved in the biological processes and pathways associated with the inflammatory response and cancer progression. A total of 10,422 peaks, containing 1,210 conpeaks involving 1,138 genes, were identified. Among the 1,138 genes, 15 were overlapped with the DEGs, and 35 miRNAs were identified to regulate those overlaps. Insulin-induced gene 1 was regulated by 9 genes in the miRNA-gene regulation network, which may indicate its importance in the progression of BC. The present study identified potential biomarkers of BC that may be useful in the diagnosis and treatment of patients with the disease. D.A. Spandidos 2017-06 2017-04-03 /pmc/articles/PMC5453034/ /pubmed/28599414 http://dx.doi.org/10.3892/ol.2017.5977 Text en Copyright: © Jiang et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. |
spellingShingle | Articles Jiang, Wenhua Liu, Pengfei Li, Xiaodong G9A performs important roles in the progression of breast cancer through upregulating its targets |
title | G9A performs important roles in the progression of breast cancer through upregulating its targets |
title_full | G9A performs important roles in the progression of breast cancer through upregulating its targets |
title_fullStr | G9A performs important roles in the progression of breast cancer through upregulating its targets |
title_full_unstemmed | G9A performs important roles in the progression of breast cancer through upregulating its targets |
title_short | G9A performs important roles in the progression of breast cancer through upregulating its targets |
title_sort | g9a performs important roles in the progression of breast cancer through upregulating its targets |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453034/ https://www.ncbi.nlm.nih.gov/pubmed/28599414 http://dx.doi.org/10.3892/ol.2017.5977 |
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