OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes

  title={OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes},
  author={Piazza Rocco and Ramazzotti Daniele and Spinelli Roberta and Pirola Alessandra and De Sano Luca and Ferrari Pierangelo and Magistroni Vera and Cordani Nicoletta and Sharma Nitesh and Gambacorti-Passerini Carlo},
  journal={Scientific Reports},
The complicated, evolving landscape of cancer mutations poses a formidable challenge to identify cancer genes among the large lists of mutations typically generated in NGS experiments. The ability to prioritize these variants is therefore of paramount importance. To address this issue we developed OncoScore, a text-mining tool that ranks genes according to their association with cancer, based on available biomedical literature. Receiver operating characteristic curve and the area under the… 

OncoScore: an R package to measure the oncogenic potential of genes.

OncoScore can scan the biomedical literature with dynamically updatable web queries and measure the association to cancer of each gene by considering their citations, resulting in a score that is measuring the strength of the association of the genes to cancer at the time of the analysis.

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RBM5 as a putative tumor suppressor gene for lung cancer.

  • L. SutherlandKe WangA. Robinson
  • Biology
    Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer
  • 2010
To more thoroughly assess the potential involvement of RBM5 as a lung cancer regulatory protein, more research is required regarding (a) the expression of not only full-length R BM5 but all of the alternate variants associated with the locus, in relation to histologic subtype and smoking history, and (b) the mutation status of various genes within the transforming growth factor-alpha signaling pathway.

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The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.

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Atypical chronic myeloid leukemia (aCML) shares clinical and laboratory features with CML, but it lacks the BCR-ABL1 fusion. We performed exome sequencing of eight aCMLs and identified somatic

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It is demonstrated that whole-exome sequencing data can be analyzed for comprehensively monitoring somatic copy number alterations (CNAs) by benchmarking the technique against conventional array CGH and showing that targeted exome sequencing reliably identifies CNAs that are common in advanced prostate cancer.

Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia

JMML was characterized by a paucity of gene mutations with somatic or germline RAS pathway involvement in 82 cases, and the SETBP1 and JAK3 genes were among common targets for secondary mutations.

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The results point towards a possible link between BRMS1 expression and apoptosis in human breast cancer through a relationship with the expression of genes belonging to the X-chromosome RBM family.

Recurrent ETNK1 mutations in atypical chronic myeloid leukemia.

This study shows for the first time the evidence of recurrent somatic ETNK1 mutations in the context of myeloproliferative/myelodysplastic disorders.