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Gene Expression Regulation, Neoplastic

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Transfer learning with convolutional neural networks for cancer survival prediction using gene-expression data.

PloS one
Precision medicine in oncology aims at obtaining data from heterogeneous sources to have a precise estimation of a given patient's state and prognosis. With the purpose of advancing to personalized medicine framework, accurate diagnoses allow prescri...

Prediction of tumor location in prostate cancer tissue using a machine learning system on gene expression data.

BMC bioinformatics
BACKGROUND: Finding the tumor location in the prostate is an essential pathological step for prostate cancer diagnosis and treatment. The location of the tumor - the laterality - can be unilateral (the tumor is affecting one side of the prostate), or...

Identification of a novel gene signature for the prediction of recurrence in HCC patients by machine learning of genome-wide databases.

Scientific reports
Hepatocellular carcinoma (HCC) is a common malignant tumor in China. In the present study, we aimed to construct and verify a prediction model of recurrence in HCC patients using databases (TCGA, AMC and Inserm) and machine learning methods and obtai...

Collective effects of long-range DNA methylations predict gene expressions and estimate phenotypes in cancer.

Scientific reports
DNA methylation of various genomic regions has been found to be associated with gene expression in diverse biological contexts. However, most genome-wide studies have focused on the effect of (1) methylation in cis, not in trans and (2) a single CpG,...

Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression.

Scientific reports
Welding generates and releases fumes that are hazardous to human health. Welding fumes (WFs) are a complex mix of metallic oxides, fluorides and silicates that can cause or exacerbate health problems in exposed individuals. In particular, WF inhalati...

Application of Machine Learning in Developing a Novelty Five-Pseudogene Signature to Predict Prognosis of Head and Neck Squamous Cell Carcinoma: A New Aspect of "Junk Genes" in Biomedical Practice.

DNA and cell biology
Head and neck squamous cell carcinoma (HNSCC) is the sixth malignancy, which is characterized by poor prognosis or high mortality because of the lack of predicting markers. Aberrant cancer pseudogenes have been found predictive for prognosis. We aim ...

A deep learning image-based intrinsic molecular subtype classifier of breast tumors reveals tumor heterogeneity that may affect survival.

Breast cancer research : BCR
BACKGROUND: Breast cancer intrinsic molecular subtype (IMS) as classified by the expression-based PAM50 assay is considered a strong prognostic feature, even when controlled for by standard clinicopathological features such as age, grade, and nodal s...

A six‑gene support vector machine classifier contributes to the diagnosis of pediatric septic shock.

Molecular medicine reports
Septic shock is induced by an uncontrolled inflammatory immune response to pathogens and the survival rate of patients with pediatric septic shock (PSS) is particularly low, with a mortality rate of 25‑50%. The present study explored the mechanisms o...

Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy.

Clinical cancer research : an official journal of the American Association for Cancer Research
PURPOSE: Tumor genomic features have been of particular interest because of their potential impact on the tumor immune microenvironment and response to immunotherapy. Due to the substantial heterogeneity, an integrative approach incorporating diverse...