Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics
Background: Achaete-scute homolog 1 transcription factors were important in the differentiation of neuronal-like glioblastoma (GBM) cancer stem cells (CSCs). To gain a better understanding of the role of ASCL1 in GBM, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) da...
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| Format: | Article |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.938712/full |
| _version_ | 1811259619740221440 |
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| author | Na Zhang Jie Zhang Zhihong Liu Tushuai Li Tushuai Li |
| author_facet | Na Zhang Jie Zhang Zhihong Liu Tushuai Li Tushuai Li |
| author_sort | Na Zhang |
| collection | DOAJ |
| description | Background: Achaete-scute homolog 1 transcription factors were important in the differentiation of neuronal-like glioblastoma (GBM) cancer stem cells (CSCs). To gain a better understanding of the role of ASCL1 in GBM, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data can be analyzed to construct their gene transcription regulation network.Methods: GSE87618 was downloaded from the Gene Expression Omnibus, which is a famous database, in the field of biology. The filtered clean reads were mapped to the human genome utilizing the software of bowtie2. Then, differential peak analysis was performed by diffbind. Finally, the annotated gene functions and signaling pathways were investigated by Gene ontology function and kyoto encyclopedia of genes genomes (KEGG) pathway enrichment analysis. Moreover, the protein–protein interaction network (PPI) analysis of genes obtained from ASCL1 was carried out to explore the hub genes influenced by ASCL1.Results: A total of 516 differential peaks were selected. GO analysis of functions revealed that promoter, untranslated region (UTR), exon, intron, and intergenic genes were mainly enriched in biological pathways such as keratinization, regulation of cAMP metabolic process, blood coagulation, fibrin clot formation, midgut development, and synapse assembly. Genes were mainly enriched in KEGG pathways including pentose phosphate pathway, glycosphingolipid biosynthesis—globo and isoglobo series, ECM–receptor interaction, and adherens junction. In total, 244 nodes and 475 interaction pairs were included in the PPI network with the hub genes including EGFR, CTNNB1, and SPTAN1.Conclusion: EGFR, SPTAN1, and CTNN1B might be the potential down-stream genes of ASCL1 in GBM development, and CTNN1B might make contributions to GBM progression on regulating the cAMP pathway. |
| first_indexed | 2024-04-12T18:34:24Z |
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| id | doaj.art-d9a5ed9edb8f4b9b988f9fa97fd99ac3 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T18:34:24Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-d9a5ed9edb8f4b9b988f9fa97fd99ac32022-12-22T03:20:59ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-09-011310.3389/fgene.2022.938712938712Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformaticsNa Zhang0Jie Zhang1Zhihong Liu2Tushuai Li3Tushuai Li4School of Food and Bioengineering, Xuzhou University of Technology, Jiangsu, Xuzhou, ChinaSchool of Biology and Food Engineering, Changshu Institute of Technology, Jiangsu, Suzhou, ChinaThe State Key Laboratory of Pharmaceutical Biotechnology, Medical School, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, ChinaSchool of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, ChinaWuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, ChinaBackground: Achaete-scute homolog 1 transcription factors were important in the differentiation of neuronal-like glioblastoma (GBM) cancer stem cells (CSCs). To gain a better understanding of the role of ASCL1 in GBM, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data can be analyzed to construct their gene transcription regulation network.Methods: GSE87618 was downloaded from the Gene Expression Omnibus, which is a famous database, in the field of biology. The filtered clean reads were mapped to the human genome utilizing the software of bowtie2. Then, differential peak analysis was performed by diffbind. Finally, the annotated gene functions and signaling pathways were investigated by Gene ontology function and kyoto encyclopedia of genes genomes (KEGG) pathway enrichment analysis. Moreover, the protein–protein interaction network (PPI) analysis of genes obtained from ASCL1 was carried out to explore the hub genes influenced by ASCL1.Results: A total of 516 differential peaks were selected. GO analysis of functions revealed that promoter, untranslated region (UTR), exon, intron, and intergenic genes were mainly enriched in biological pathways such as keratinization, regulation of cAMP metabolic process, blood coagulation, fibrin clot formation, midgut development, and synapse assembly. Genes were mainly enriched in KEGG pathways including pentose phosphate pathway, glycosphingolipid biosynthesis—globo and isoglobo series, ECM–receptor interaction, and adherens junction. In total, 244 nodes and 475 interaction pairs were included in the PPI network with the hub genes including EGFR, CTNNB1, and SPTAN1.Conclusion: EGFR, SPTAN1, and CTNN1B might be the potential down-stream genes of ASCL1 in GBM development, and CTNN1B might make contributions to GBM progression on regulating the cAMP pathway.https://www.frontiersin.org/articles/10.3389/fgene.2022.938712/fullachaete-scute homolog 1 geneglioblastomasbioinformaticsChIP-seqsignaling pathways |
| spellingShingle | Na Zhang Jie Zhang Zhihong Liu Tushuai Li Tushuai Li Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics Frontiers in Genetics achaete-scute homolog 1 gene glioblastomas bioinformatics ChIP-seq signaling pathways |
| title | Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics |
| title_full | Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics |
| title_fullStr | Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics |
| title_full_unstemmed | Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics |
| title_short | Identification of signaling pathways associated with achaete-scute homolog 1 in glioblastomas through ChIP-seq data bioinformatics |
| title_sort | identification of signaling pathways associated with achaete scute homolog 1 in glioblastomas through chip seq data bioinformatics |
| topic | achaete-scute homolog 1 gene glioblastomas bioinformatics ChIP-seq signaling pathways |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.938712/full |
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