The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach
<p dir="ltr">Breast cancer (BC) is one of the leading causes of cancer-related death among women worldwide, and claudin-low breast cancer (CLBC) is a subtype of BC that remains poorly described. This study aimed to identify upregulated genes and significant pathways involved in CLBC....
محفوظ في:
| المؤلف الرئيسي: | |
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| منشور في: |
2020
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| الموضوعات: | |
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إضافة وسم
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| _version_ | 1864513550035189760 |
|---|---|
| author | Hatem Zayed (835448) |
| author_facet | Hatem Zayed (835448) |
| author_role | author |
| dc.creator.none.fl_str_mv | Hatem Zayed (835448) |
| dc.date.none.fl_str_mv | 2020-12-01T00:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1016/j.compbiomed.2020.103806 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/The_identification_of_highly_upregulated_genes_in_claudin-low_breast_cancer_through_an_integrative_bioinformatics_approach/24287971 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biomedical and clinical sciences Oncology and carcinogenesis Health sciences Health services and systems Breast cancer Microarray Claudin-low breast cancer Biomarkers Functional enrichment analysis Differential gene expression |
| dc.title.none.fl_str_mv | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Breast cancer (BC) is one of the leading causes of cancer-related death among women worldwide, and claudin-low breast cancer (CLBC) is a subtype of BC that remains poorly described. This study aimed to identify upregulated genes and significant pathways involved in CLBC. The SUM159 cell line is derived from human CLBC tissue; the GSE50697 dataset contains three replicates of SUM159 cells treated with pBabe puro miR-203 and three replicates of control SUM159 cells (pBabe puro). The data were normalized and upregulated, and downregulated genes were identified based on the logFC values. Gene Ontology (GO) and pathway analysis identified the most significant pathways and genes involved in CLBC pathogenesis. A total of 156 significant genes were identified (69 upregulated genes and 64 downregulated genes). The upregulated genes were the focus of this study, from the pathway analysis, the senescence-associated secretory phenotype, which involves the CXCL8, IL1A, and IL6 genes, was found to be mapped through more than one pathway (WikiPathways and Reactome). From the refined GO analysis, using MetaCore, Cortellis solution software, the IL-13 signaling pathway was identified; this pathway includes the IL6, CXCL8, VEGF-C, NRG1, and EREG genes, which were mapped as hub genes in several pathogenesis pathways. From the survival analysis, high levels of IL6, CXCL8, and EREG were related to high survival rates, and low levels of VEGFC and NRG1 were related to high survival rates. The IL6 and CXCL8 genes were the most significant and the most highly represented in the GO and refined GO analyses. This study sheds light on the molecular pathology of CLBC and might provide a potential biomarkers for the treatment of CLBC.</p><h2>Other Information</h2><p dir="ltr">Published in: Computers in Biology and Medicine<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1016/j.compbiomed.2020.103806" target="_blank">https://dx.doi.org/10.1016/j.compbiomed.2020.103806</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_aa8ac5b2a657951de357585a34192636 |
| identifier_str_mv | 10.1016/j.compbiomed.2020.103806 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/24287971 |
| publishDate | 2020 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approachHatem Zayed (835448)Biomedical and clinical sciencesOncology and carcinogenesisHealth sciencesHealth services and systemsBreast cancerMicroarrayClaudin-low breast cancerBiomarkersFunctional enrichment analysisDifferential gene expression<p dir="ltr">Breast cancer (BC) is one of the leading causes of cancer-related death among women worldwide, and claudin-low breast cancer (CLBC) is a subtype of BC that remains poorly described. This study aimed to identify upregulated genes and significant pathways involved in CLBC. The SUM159 cell line is derived from human CLBC tissue; the GSE50697 dataset contains three replicates of SUM159 cells treated with pBabe puro miR-203 and three replicates of control SUM159 cells (pBabe puro). The data were normalized and upregulated, and downregulated genes were identified based on the logFC values. Gene Ontology (GO) and pathway analysis identified the most significant pathways and genes involved in CLBC pathogenesis. A total of 156 significant genes were identified (69 upregulated genes and 64 downregulated genes). The upregulated genes were the focus of this study, from the pathway analysis, the senescence-associated secretory phenotype, which involves the CXCL8, IL1A, and IL6 genes, was found to be mapped through more than one pathway (WikiPathways and Reactome). From the refined GO analysis, using MetaCore, Cortellis solution software, the IL-13 signaling pathway was identified; this pathway includes the IL6, CXCL8, VEGF-C, NRG1, and EREG genes, which were mapped as hub genes in several pathogenesis pathways. From the survival analysis, high levels of IL6, CXCL8, and EREG were related to high survival rates, and low levels of VEGFC and NRG1 were related to high survival rates. The IL6 and CXCL8 genes were the most significant and the most highly represented in the GO and refined GO analyses. This study sheds light on the molecular pathology of CLBC and might provide a potential biomarkers for the treatment of CLBC.</p><h2>Other Information</h2><p dir="ltr">Published in: Computers in Biology and Medicine<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1016/j.compbiomed.2020.103806" target="_blank">https://dx.doi.org/10.1016/j.compbiomed.2020.103806</a></p>2020-12-01T00:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1016/j.compbiomed.2020.103806https://figshare.com/articles/journal_contribution/The_identification_of_highly_upregulated_genes_in_claudin-low_breast_cancer_through_an_integrative_bioinformatics_approach/24287971CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/242879712020-12-01T00:00:00Z |
| spellingShingle | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach Hatem Zayed (835448) Biomedical and clinical sciences Oncology and carcinogenesis Health sciences Health services and systems Breast cancer Microarray Claudin-low breast cancer Biomarkers Functional enrichment analysis Differential gene expression |
| status_str | publishedVersion |
| title | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| title_full | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| title_fullStr | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| title_full_unstemmed | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| title_short | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| title_sort | The identification of highly upregulated genes in claudin-low breast cancer through an integrative bioinformatics approach |
| topic | Biomedical and clinical sciences Oncology and carcinogenesis Health sciences Health services and systems Breast cancer Microarray Claudin-low breast cancer Biomarkers Functional enrichment analysis Differential gene expression |