Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values
Background: Breast cancer is the second leading cause of death in women worldwide. Notwithstanding all medical advances, nowadays, we confront the emergency demands of certain solutions solving this dilemma. An effective approach may be recognizing mRNA/miRNA expression profiles in breast cancer. Ma...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-01-01
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| Series: | Informatics in Medicine Unlocked |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S235291482030575X |
| _version_ | 1818171930156466176 |
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| author | Amir Mehrgou Shima Ebadollahi Behnam Jameie Shahram Teimourian |
| author_facet | Amir Mehrgou Shima Ebadollahi Behnam Jameie Shahram Teimourian |
| author_sort | Amir Mehrgou |
| collection | DOAJ |
| description | Background: Breast cancer is the second leading cause of death in women worldwide. Notwithstanding all medical advances, nowadays, we confront the emergency demands of certain solutions solving this dilemma. An effective approach may be recognizing mRNA/miRNA expression profiles in breast cancer. Material & methods: Through searching Gene Expression Omnibus (GEO) database, and using GSE29174 and GSE58606, the GEO2R online tool, and the Limma package, (common) differentially expressed genes (DEGs) and miRNAs (DEMs) for all breast cancer subtypes are designated, respectively. All DEGs-DEMs interactions are found and visualized via miRTarBase and Cytoscape. Considering the STRING database and Cytohubba plugin, the protein-protein interactions (PPI) are plotted. Via R packages, and Kaplan-Meier Plotter, functional enrichment and survival analysis are conducted, respectively. Then, common DEGs validation is carried out by GSE45827 and the final PPI networks with diagnostic and prognostic values were plotted. Ultimately, for more verification (strictly) validated common DEGs were investigated using the GEPIA. Results: The proprietary and common DEGs and DEMs for all breast cancer subtypes are discovered. Afterward, DEGs and DEMs interactions are plotted. Furthermore, diagnosis- and prognosis-applicable gene expression profiles, novel expression change in four genes, and in two microRNAs, and one contingent new gene-miRNA interaction in breast cancer development and prognosis are ascertained. Conclusion: Pursuant to the discovered profiles, and our novel findings, they may be the potential targets for upcoming research as to prognosis, diagnosis, and targeted therapy in breast cancer. |
| first_indexed | 2024-12-11T19:04:32Z |
| format | Article |
| id | doaj.art-82d3e049bfae478882d1510da91844c9 |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-12-11T19:04:32Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-82d3e049bfae478882d1510da91844c92022-12-22T00:53:56ZengElsevierInformatics in Medicine Unlocked2352-91482020-01-0120100425Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic valuesAmir Mehrgou0Shima Ebadollahi1Behnam Jameie2Shahram Teimourian3Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, IranDepartment of Biochemistry and Biophysics, Faculty of Medicine, Babol University of Medical Sciences, Babol, IranNeuroscience Research Center, Iran University of Medical Sciences, Tehran, IranDepartment of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran; Corresponding author.Background: Breast cancer is the second leading cause of death in women worldwide. Notwithstanding all medical advances, nowadays, we confront the emergency demands of certain solutions solving this dilemma. An effective approach may be recognizing mRNA/miRNA expression profiles in breast cancer. Material & methods: Through searching Gene Expression Omnibus (GEO) database, and using GSE29174 and GSE58606, the GEO2R online tool, and the Limma package, (common) differentially expressed genes (DEGs) and miRNAs (DEMs) for all breast cancer subtypes are designated, respectively. All DEGs-DEMs interactions are found and visualized via miRTarBase and Cytoscape. Considering the STRING database and Cytohubba plugin, the protein-protein interactions (PPI) are plotted. Via R packages, and Kaplan-Meier Plotter, functional enrichment and survival analysis are conducted, respectively. Then, common DEGs validation is carried out by GSE45827 and the final PPI networks with diagnostic and prognostic values were plotted. Ultimately, for more verification (strictly) validated common DEGs were investigated using the GEPIA. Results: The proprietary and common DEGs and DEMs for all breast cancer subtypes are discovered. Afterward, DEGs and DEMs interactions are plotted. Furthermore, diagnosis- and prognosis-applicable gene expression profiles, novel expression change in four genes, and in two microRNAs, and one contingent new gene-miRNA interaction in breast cancer development and prognosis are ascertained. Conclusion: Pursuant to the discovered profiles, and our novel findings, they may be the potential targets for upcoming research as to prognosis, diagnosis, and targeted therapy in breast cancer.http://www.sciencedirect.com/science/article/pii/S235291482030575XBioinformatics analysisDifferentially expressed genesDifferentially expressed microRNAsDiagnostic gene expression profilePrognostic gene expression profileBreast cancer subtypes |
| spellingShingle | Amir Mehrgou Shima Ebadollahi Behnam Jameie Shahram Teimourian Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values Informatics in Medicine Unlocked Bioinformatics analysis Differentially expressed genes Differentially expressed microRNAs Diagnostic gene expression profile Prognostic gene expression profile Breast cancer subtypes |
| title | Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values |
| title_full | Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values |
| title_fullStr | Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values |
| title_full_unstemmed | Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values |
| title_short | Analysis of subtype-specific and common Gene/MiRNA expression profiles of four main breast cancer subtypes using bioinformatic approach; Characterization of four genes, and two MicroRNAs with possible diagnostic and prognostic values |
| title_sort | analysis of subtype specific and common gene mirna expression profiles of four main breast cancer subtypes using bioinformatic approach characterization of four genes and two micrornas with possible diagnostic and prognostic values |
| topic | Bioinformatics analysis Differentially expressed genes Differentially expressed microRNAs Diagnostic gene expression profile Prognostic gene expression profile Breast cancer subtypes |
| url | http://www.sciencedirect.com/science/article/pii/S235291482030575X |
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