Full metadata record
DC Field | Value | Language |
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dc.creator | Carazo-Melo, F.(Fernando) | - |
dc.creator | Campuzano, L. (Lucía) | - |
dc.creator | Cendoya-Garmendia, X. (Xabier) | - |
dc.creator | Planes-Pedreño, F.J. (Francisco Javier) | - |
dc.creator | Rubio, A. (Ángel) | - |
dc.date.accessioned | 2022-03-02T07:33:46Z | - |
dc.date.available | 2022-03-02T07:33:46Z | - |
dc.date.issued | 2019 | - |
dc.identifier.citation | Carazo Melo, F.(Fernando); Campuzano, L. (Lucía); Cendoya, X. (Xabier); et al. "TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer". GigaScience. 8 (4), 2019, giz021 | es |
dc.identifier.issn | 2047-217X | - |
dc.identifier.uri | https://hdl.handle.net/10171/62965 | - |
dc.description.abstract | Background Aberrant alternative splicing plays a key role in cancer development. In recent years, alternative splicing has been used as a prognosis biomarker, a therapy response biomarker, and even as a therapeutic target. Next-generation RNA sequencing has an unprecedented potential to measure the transcriptome. However, due to the complexity of dealing with isoforms, the scientific community has not sufficiently exploited this valuable resource in precision medicine. Findings We present TranscriptAchilles, the first large-scale tool to predict transcript biomarkers associated with gene essentiality in cancer. This application integrates 412 loss-of-function RNA interference screens of >17,000 genes, together with their corresponding whole-transcriptome expression profiling. Using this tool, we have studied which are the cancer subtypes for which alternative splicing plays a significant role to state gene essentiality. In addition, we include a case study of renal cell carcinoma that shows the biological soundness of the results. The databases, the source code, and a guide to build the platform within a Docker container are available at GitLab. The application is also available online. Conclusions TranscriptAchilles provides a user-friendly web interface to identify transcript or gene biomarkers of gene essentiality, which could be used as a starting point for a drug development project. This approach opens a wide range of translational applications in cancer. | es_ES |
dc.description.sponsorship | Research reported in this publication was supported by the Provincial Council of Gipuzkoa through the MINEDRUG project “Predicting therapy response in oncology using Big Data analysis” and the Basque Government with the grant promoting doctoral theses for young predoctoral researchers [grants PRE 2017 2 0033 to F.C. and PRE 2017 1 0327 to X.C.]. | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Oxford University Press (OUP) | es_ES |
dc.rights | info:eu-repo/semantics/openAccess | es_ES |
dc.subject | Applications in cancer | es_ES |
dc.subject | TranscriptAchilles | es_ES |
dc.subject | Alternative splicing | es_ES |
dc.subject | Prognosis biomarker | es_ES |
dc.title | TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.description.note | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. | es_ES |
dc.identifier.doi | 10.1093/gigascience/giz021 | - |
dadun.citation.number | 4 | es_ES |
dadun.citation.publicationName | GigaScience | es_ES |
dadun.citation.startingPage | giz021 | es_ES |
dadun.citation.volume | 8 | es_ES |
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