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Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN

Jonatan Linus Gabre (UGent) , Peter Merseburger (UGent) , Arne Claeys (UGent) , Joachim Siaw (UGent) , Sarah-Lee Bekaert (UGent) , Franki Speleman (UGent) , Bengt Hallberg, Ruth H Palmer and Jimmy Van den Eynden (UGent)
(2024) NAR CANCER. 6(1).
Author
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Abstract
Neuroblastoma (NB) is the most common cancer in infancy with an urgent need for more efficient targeted therapies. The development of novel (combinatorial) treatment strategies relies on extensive explorations of signaling perturbations in neuroblastoma cell lines, using RNA-Seq or other high throughput technologies (e.g. phosphoproteomics). This typically requires dedicated bioinformatics support, which is not always available. Additionally, while data from published studies are highly valuable and raw data (e.g. fastq files) are nowadays released in public repositories, data processing is time-consuming and again difficult without bioinformatics support. To facilitate NB research, more user-friendly and immediately accessible platforms are needed to explore newly generated as well as existing high throughput data. To make this possible, we developed an interactive data centralization and visualization web application, called CLEAN (the Cell Line Explorer web Application of Neuroblastoma data; https://ccgg.ugent.be/shiny/clean/). By focusing on the regulation of the DNA damage response, a therapeutic target of major interest in neuroblastoma, we demonstrate how CLEAN can be used to gain novel mechanistic insights and identify putative drug targets in neuroblastoma.
Keywords
Cancer Research, Oncology

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Citation

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MLA
Gabre, Jonatan Linus, et al. “Preclinical Exploration of the DNA Damage Response Pathway Using the Interactive Neuroblastoma Cell Line Explorer CLEAN.” NAR CANCER, vol. 6, no. 1, Oxford University Press (OUP), 2024, doi:10.1093/narcan/zcad062.
APA
Gabre, J. L., Merseburger, P., Claeys, A., Siaw, J., Bekaert, S.-L., Speleman, F., … Van den Eynden, J. (2024). Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN. NAR CANCER, 6(1). https://doi.org/10.1093/narcan/zcad062
Chicago author-date
Gabre, Jonatan Linus, Peter Merseburger, Arne Claeys, Joachim Siaw, Sarah-Lee Bekaert, Franki Speleman, Bengt Hallberg, Ruth H Palmer, and Jimmy Van den Eynden. 2024. “Preclinical Exploration of the DNA Damage Response Pathway Using the Interactive Neuroblastoma Cell Line Explorer CLEAN.” NAR CANCER 6 (1). https://doi.org/10.1093/narcan/zcad062.
Chicago author-date (all authors)
Gabre, Jonatan Linus, Peter Merseburger, Arne Claeys, Joachim Siaw, Sarah-Lee Bekaert, Franki Speleman, Bengt Hallberg, Ruth H Palmer, and Jimmy Van den Eynden. 2024. “Preclinical Exploration of the DNA Damage Response Pathway Using the Interactive Neuroblastoma Cell Line Explorer CLEAN.” NAR CANCER 6 (1). doi:10.1093/narcan/zcad062.
Vancouver
1.
Gabre JL, Merseburger P, Claeys A, Siaw J, Bekaert S-L, Speleman F, et al. Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN. NAR CANCER. 2024;6(1).
IEEE
[1]
J. L. Gabre et al., “Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN,” NAR CANCER, vol. 6, no. 1, 2024.
@article{01HKYM68KWRE9E69S6AC5GXC3T,
  abstract     = {{Neuroblastoma (NB) is the most common cancer in infancy with an urgent need for more efficient targeted therapies. The development of novel (combinatorial) treatment strategies relies on extensive explorations of signaling perturbations in neuroblastoma cell lines, using RNA-Seq or other high throughput technologies (e.g. phosphoproteomics). This typically requires dedicated bioinformatics support, which is not always available. Additionally, while data from published studies are highly valuable and raw data (e.g. fastq files) are nowadays released in public repositories, data processing is time-consuming and again difficult without bioinformatics support. To facilitate NB research, more user-friendly and immediately accessible platforms are needed to explore newly generated as well as existing high throughput data. To make this possible, we developed an interactive data centralization and visualization web application, called CLEAN (the Cell Line Explorer web Application of Neuroblastoma data; https://ccgg.ugent.be/shiny/clean/). By focusing on the regulation of the DNA damage response, a therapeutic target of major interest in neuroblastoma, we demonstrate how CLEAN can be used to gain novel mechanistic insights and identify putative drug targets in neuroblastoma.}},
  articleno    = {{zcad062}},
  author       = {{Gabre, Jonatan Linus and Merseburger, Peter and Claeys, Arne and Siaw, Joachim and Bekaert, Sarah-Lee and Speleman, Franki and Hallberg, Bengt and Palmer, Ruth H and Van den Eynden, Jimmy}},
  issn         = {{2632-8674}},
  journal      = {{NAR CANCER}},
  keywords     = {{Cancer Research,Oncology}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{8}},
  publisher    = {{Oxford University Press (OUP)}},
  title        = {{Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN}},
  url          = {{http://doi.org/10.1093/narcan/zcad062}},
  volume       = {{6}},
  year         = {{2024}},
}
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