Utilizing Protein Structure to Identify Non-Random Somatic Mutations [PDF]
, 2013 Motivation: Human cancer is caused by the accumulation of somatic mutations in tumor suppressors and oncogenes within the genome. In the case of oncogenes, recent theory suggests that there are only a few key "driver" mutations responsible for tumorigenesis. As there have been significant pharmacological successes in developing drugs that treat cancers
arxiv +1 more source
TAF2: A potential oncogene for hepatocellular carcinoma [PDF]
, 2017 Astrocyte Elevated Gene 1 (AEG1) is an oncogene for hepatocellular carcinoma (HCC). Its role in HCC pathogenesis has been well studied. A pan cancer analysis of gene expression in multiple databases identified TATA-box binding protein associated factor 2
Chidambaranathan Reghupaty, Saranya
core +1 more source
Cadherin composition and multicellular aggregate invasion in organotypic models of epithelial ovarian cancer intraperitoneal metastasis. [PDF]
, 2017 During epithelial ovarian cancer (EOC) progression, intraperitoneally disseminating tumor cells and multicellular aggregates (MCAs) present in ascites fluid adhere to the peritoneum and induce retraction of the peritoneal mesothelial monolayer prior to ...
Alber, M +6 more
core +2 more sources
Variance function estimation in quantitative mass spectrometry with application to iTRAQ labeling [PDF]
Annals of Applied Statistics 2013, Vol. 7, No. 1, 1-24, 2013 This paper describes and compares two methods for estimating the variance function associated with iTRAQ (isobaric tag for relative and absolute quantitation) isotopic labeling in quantitative mass spectrometry based proteomics. Measurements generated by the mass spectrometer are proportional to the concentration of peptides present in the biological ...
arxiv +1 more source
TGF-β signaling links E-cadherin loss to suppression of nucleotide excision repair. [PDF]
, 2016 E-cadherin is a cell adhesion molecule best known for its function in suppressing tumor progression and metastasis. Here we show that E-cadherin promotes nucleotide excision repair through positively regulating the expression of xeroderma pigmentosum ...
Barcellos-Hoff, MH +3 more
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Adenoid cystic carcinoma: emerging role of translocations and gene fusions. [PDF]
, 2016 Adenoid cystic carcinoma (ACC), the second most common salivary gland malignancy, is notorious for poor prognosis, which reflects the propensity of ACC to progress to clinically advanced metastatic disease.
Brait, Mariana +5 more
core +3 more sources
Integrative multi-omics module network inference with Lemon-Tree [PDF]
PLoS Comput Biol 11(2): e1003983 (2015), 2014 Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points of a dynamic process.
arxiv +1 more source
Targeting colorectal cancer via its microenvironment by inhibiting IGF-1 receptor-insulin receptor substrate and STAT3 signaling. [PDF]
, 2016 The tumor microenvironment (TME) exerts critical pro-tumorigenic effects through cytokines and growth factors that support cancer cell proliferation, survival, motility and invasion.
Flashner-Abramson, E +6 more
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Why Mutant Allele Frequencies in Oncogenes Peak Around 0.40 and Rapidly Decrease? [PDF]
arXiv, 2016 The mutant allele frequencies in oncogenes peak around 0.40 and rapidly decrease. In this article, we explain why this is the case. Invoking a key result from mathematical analysis in our model, namely, the inverse function theorem, we estimate the selection pressures of the mutations as a function of germline allele frequencies.
arxiv
Targeting of RET oncogene by naphthalene diimide-mediated gene promoter G-quadruplex stabilization exerts anti-tumor activity in oncogene-addicted human medullary thyroid cancer [PDF]
, 2016 Medullary thyroid cancer (MTC) relies on the aberrant activation of RET proto-oncogene. Though targeted approaches (i.e., tyrosine kinase inhibitors) are available, the absence of complete responses and the onset of resistance mechanisms indicate the ...
Beretta, Giovanni L +11 more
core +1 more source