TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success
Many publicly available databases provide disease related data, that makes it possible to link genomic data to medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand of datasets covering a wide array of cancer types. Here we introduce an interactive and highly...
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| Format: | Article |
| Language: | English |
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De Gruyter
2024-12-01
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| Series: | Journal of Integrative Bioinformatics |
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| Online Access: | https://doi.org/10.1515/jib-2024-0031 |
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| author | Balogh Gabor Jorge Natasha Dupain Célia Kamal Maud Servant Nicolas Le Tourneau Christophe Stadler Peter F. Bernhart Stephan H. |
| author_facet | Balogh Gabor Jorge Natasha Dupain Célia Kamal Maud Servant Nicolas Le Tourneau Christophe Stadler Peter F. Bernhart Stephan H. |
| author_sort | Balogh Gabor |
| collection | DOAJ |
| description | Many publicly available databases provide disease related data, that makes it possible to link genomic data to medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand of datasets covering a wide array of cancer types. Here we introduce an interactive and highly automatized TCGA-based workflow that links and analyses epigenomic and transcriptomic data with treatment and survival data in order to identify possible biomarkers that indicate treatment success. TREMSUCS-TCGA is flexible with respect to type of cancer and treatment and provides standard methods for differential expression analysis or DMR detection. Furthermore, it makes it possible to examine several cancer types together in a pan-cancer type approach. Parallelisation and reproducibility of all steps is ensured with the workflowmanagement system Snakemake. TREMSUCS-TCGA produces a comprehensive single report file which holds all relevant results in descriptive and tabular form that can be explored in an interactive manner. As a showcase application we describe a comprehensive analysis of the available data for the combination of patients with squamous cell carcinomas of head and neck, cervix and lung treated with cisplatin, carboplatin and the combination of carboplatin and paclitaxel. The best ranked biomarker candidates are discussed in the light of the existing literature, indicating plausible causal relationships to the relevant cancer entities. |
| format | Article |
| id | doaj-art-95572e2bae4447ca90547ed0200ee842 |
| institution | Kabale University |
| issn | 1613-4516 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj-art-95572e2bae4447ca90547ed0200ee8422025-01-07T07:55:54ZengDe GruyterJournal of Integrative Bioinformatics1613-45162024-12-01214993810.1515/jib-2024-0031TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment successBalogh Gabor0Jorge Natasha1Dupain Célia2Kamal Maud3Servant Nicolas4Le Tourneau Christophe5Stadler Peter F.6Bernhart Stephan H.7Interdisciplinary Center of Bioinformatics, 9180Leipzig University, Härtelstraße 16-18, D-04107Leipzig, GermanyInterdisciplinary Center of Bioinformatics, 9180Leipzig University, Härtelstraße 16-18, D-04107Leipzig, GermanyDepartment of Drug Development and Innovation (D3i), Institut Curie, Paris, FranceDepartment of Drug Development and Innovation (D3i), Institut Curie, Paris, FranceInserm U900 Research Unit, Saint Cloud, FranceDepartment of Drug Development and Innovation (D3i), Institut Curie, Paris, FranceInterdisciplinary Center of Bioinformatics, 9180Leipzig University, Härtelstraße 16-18, D-04107Leipzig, GermanyInterdisciplinary Center of Bioinformatics, 9180Leipzig University, Härtelstraße 16-18, D-04107Leipzig, GermanyMany publicly available databases provide disease related data, that makes it possible to link genomic data to medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand of datasets covering a wide array of cancer types. Here we introduce an interactive and highly automatized TCGA-based workflow that links and analyses epigenomic and transcriptomic data with treatment and survival data in order to identify possible biomarkers that indicate treatment success. TREMSUCS-TCGA is flexible with respect to type of cancer and treatment and provides standard methods for differential expression analysis or DMR detection. Furthermore, it makes it possible to examine several cancer types together in a pan-cancer type approach. Parallelisation and reproducibility of all steps is ensured with the workflowmanagement system Snakemake. TREMSUCS-TCGA produces a comprehensive single report file which holds all relevant results in descriptive and tabular form that can be explored in an interactive manner. As a showcase application we describe a comprehensive analysis of the available data for the combination of patients with squamous cell carcinomas of head and neck, cervix and lung treated with cisplatin, carboplatin and the combination of carboplatin and paclitaxel. The best ranked biomarker candidates are discussed in the light of the existing literature, indicating plausible causal relationships to the relevant cancer entities.https://doi.org/10.1515/jib-2024-0031tcgasccbiomarkerprecision medicinedifferential expressiondifferentially methylated regions |
| spellingShingle | Balogh Gabor Jorge Natasha Dupain Célia Kamal Maud Servant Nicolas Le Tourneau Christophe Stadler Peter F. Bernhart Stephan H. TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success Journal of Integrative Bioinformatics tcga scc biomarker precision medicine differential expression differentially methylated regions |
| title | TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success |
| title_full | TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success |
| title_fullStr | TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success |
| title_full_unstemmed | TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success |
| title_short | TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success |
| title_sort | tremsucs tcga an integrated workflow for the identification of biomarkers for treatment success |
| topic | tcga scc biomarker precision medicine differential expression differentially methylated regions |
| url | https://doi.org/10.1515/jib-2024-0031 |
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