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Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells
BACKGROUND: Glioma is one of the most common primary malignancies in the brain or spine. The transcription factor (TF) CCAAT/enhancer binding protein beta (CEBPB) is important for maintaining the tumor initiating capacity and invasion ability. To investigate the regulation mechanism of CEBPB in glio...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054626/ https://www.ncbi.nlm.nih.gov/pubmed/27716259 http://dx.doi.org/10.1186/s12957-016-0997-z |
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author | Du, Chenghua Pan, Pan Jiang, Yan Zhang, Qiuli Bao, Jinsuo Liu, Chang |
author_facet | Du, Chenghua Pan, Pan Jiang, Yan Zhang, Qiuli Bao, Jinsuo Liu, Chang |
author_sort | Du, Chenghua |
collection | PubMed |
description | BACKGROUND: Glioma is one of the most common primary malignancies in the brain or spine. The transcription factor (TF) CCAAT/enhancer binding protein beta (CEBPB) is important for maintaining the tumor initiating capacity and invasion ability. To investigate the regulation mechanism of CEBPB in glioma, microarray data GSE47352 was analyzed. METHODS: GSE47352 was downloaded from Gene Expression Omnibus, including three samples of SNB19 human glioma cells transduced with non-target control small hairpin RNA (shRNA) lentiviral vectors for 72 h (normal glioma cells) and three samples of SNB19 human glioma cells transduced with CEBPB shRNA lentiviral vectors for 72 h (CEBPB-silenced glioma cells). The differentially expressed genes (DEGs) were screened using limma package and then annotated. Afterwards, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) software was applied to perform enrichment analysis for the DEGs. Furthermore, the protein-protein interaction (PPI) network and transcriptional regulatory network were constructed using Cytoscape software. RESULTS: Total 529 DEGs were identified in the normal glioma cells compared with the CEBPB-silenced glioma cells, including 336 up-regulated and 193 down-regulated genes. The significantly enriched pathways included chemokine signaling pathway (which involved CCL2), focal adhesion (which involved THBS1 and THBS2), TGF-beta signaling pathway (which involved THBS1, THBS2, SMAD5, and SMAD6) and chronic myeloid leukemia (which involved TGFBR2 and CCND1). In the PPI network, CCND1 (degree = 29) and CCL2 (degree = 12) were hub nodes. Additionally, CEBPB and TCF12 might function in glioma through targeting others (CEBPB → TCF12, CEBPB → TGFBR2, and TCF12 → TGFBR2). CONCLUSIONS: CEBPB might act in glioma by regulating CCL2, CCND1, THBS1, THBS2, SMAD5, SMAD6, TGFBR2, and TCF12. |
format | Online Article Text |
id | pubmed-5054626 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-50546262016-10-19 Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells Du, Chenghua Pan, Pan Jiang, Yan Zhang, Qiuli Bao, Jinsuo Liu, Chang World J Surg Oncol Research BACKGROUND: Glioma is one of the most common primary malignancies in the brain or spine. The transcription factor (TF) CCAAT/enhancer binding protein beta (CEBPB) is important for maintaining the tumor initiating capacity and invasion ability. To investigate the regulation mechanism of CEBPB in glioma, microarray data GSE47352 was analyzed. METHODS: GSE47352 was downloaded from Gene Expression Omnibus, including three samples of SNB19 human glioma cells transduced with non-target control small hairpin RNA (shRNA) lentiviral vectors for 72 h (normal glioma cells) and three samples of SNB19 human glioma cells transduced with CEBPB shRNA lentiviral vectors for 72 h (CEBPB-silenced glioma cells). The differentially expressed genes (DEGs) were screened using limma package and then annotated. Afterwards, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) software was applied to perform enrichment analysis for the DEGs. Furthermore, the protein-protein interaction (PPI) network and transcriptional regulatory network were constructed using Cytoscape software. RESULTS: Total 529 DEGs were identified in the normal glioma cells compared with the CEBPB-silenced glioma cells, including 336 up-regulated and 193 down-regulated genes. The significantly enriched pathways included chemokine signaling pathway (which involved CCL2), focal adhesion (which involved THBS1 and THBS2), TGF-beta signaling pathway (which involved THBS1, THBS2, SMAD5, and SMAD6) and chronic myeloid leukemia (which involved TGFBR2 and CCND1). In the PPI network, CCND1 (degree = 29) and CCL2 (degree = 12) were hub nodes. Additionally, CEBPB and TCF12 might function in glioma through targeting others (CEBPB → TCF12, CEBPB → TGFBR2, and TCF12 → TGFBR2). CONCLUSIONS: CEBPB might act in glioma by regulating CCL2, CCND1, THBS1, THBS2, SMAD5, SMAD6, TGFBR2, and TCF12. BioMed Central 2016-10-06 /pmc/articles/PMC5054626/ /pubmed/27716259 http://dx.doi.org/10.1186/s12957-016-0997-z Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Du, Chenghua Pan, Pan Jiang, Yan Zhang, Qiuli Bao, Jinsuo Liu, Chang Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells |
title | Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells |
title_full | Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells |
title_fullStr | Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells |
title_full_unstemmed | Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells |
title_short | Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells |
title_sort | microarray data analysis to identify crucial genes regulated by cebpb in human snb19 glioma cells |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054626/ https://www.ncbi.nlm.nih.gov/pubmed/27716259 http://dx.doi.org/10.1186/s12957-016-0997-z |
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