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View article: Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening
Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening Open
Background Advancements in transcriptomic profiling have led to the emergence of new challenges regarding data integration and interpretability. Variability between measurement platforms makes it difficult to compare between cohorts, and l…
View article: Additional file 3 of Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening
Additional file 3 of Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening Open
Additional file 3. Top gene pairs (HER2 status). This file contains raw calculated data of the top 100 gene pairs and feature selection scores for the HER2-positive and HER2-negative comparison.
View article: Additional file 9 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 9 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 9. Gene ontology enrichment analysis in the yellow group.
View article: Additional file 1 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 1 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 1. DMPs between blue and pink groups.
View article: Additional file 6 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 6 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 6. DMPs between pink and yellow groups.
View article: Additional file 5 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 5 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 5. DMPs between pink and yellow groups.
View article: Additional file 8 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 8 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 8. Gene ontology enrichment analysis in the pink group.
View article: Additional file 4 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 4 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 4. DMRs between blue and yellow groups.
View article: Additional file 3 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 3 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 3. DMPs between blue and yellow groups.
View article: Additional file 10 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 10 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 10. DMPs in the yellow group.
View article: Additional file 2 of Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening
Additional file 2 of Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening Open
Additional file 2. Top gene pairs (ER status). This file contains raw calculated data of the top 100 gene pairs and feature selection scores for the ER-positive and ER-negative comparison.
View article: Additional file 1 of Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening
Additional file 1 of Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening Open
Additional file 1. Top gene pairs (breast cancer vs control). This file contains raw calculated data of the top 100 gene pairs and feature selection scores for the breast cancer and control comparison.
View article: Additional file 2 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 2 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 2. DMRs between blue and pink groups.
View article: Additional file 7 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes
Additional file 7 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes Open
Additional file 7. Gene ontology enrichment analysis in the blue group.
View article: Maternal Low-Fat Diet Programs the Hepatic Epigenome despite Exposure to an Obesogenic Postnatal Diet
Maternal Low-Fat Diet Programs the Hepatic Epigenome despite Exposure to an Obesogenic Postnatal Diet Open
Obesity and metabolic disease present a danger to long-term health outcomes. It has been hypothesized that epigenetic marks established during early life might program individuals and have either beneficial or harmful consequences later in…
View article: The Efficacy of miR-20a as a Diagnostic and Prognostic Biomarker for Colorectal Cancer: A Systematic Review and Meta-Analysis
The Efficacy of miR-20a as a Diagnostic and Prognostic Biomarker for Colorectal Cancer: A Systematic Review and Meta-Analysis Open
Background: MicroRNAs have altered expression levels in various diseases and may play an important role in the diagnosis and prognosis of colorectal cancer (CRC). Methods: We systemically reviewed and quantitatively synthesized the scienti…
View article: Maternal and Post-Weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts
Maternal and Post-Weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts Open
Calorie-dense high-fat diets (HF) are associated with detrimental health outcomes, including obesity, cardiovascular disease, and diabetes. Both pre- and post-natal HF diets have been hypothesized to negatively impact long-term metabolic h…
View article: Feasibility Outcomes of a Pilot Randomized Clinical Trial to Increase Cruciferous and Green Leafy Vegetable Intake in Posttreatment Head and Neck Cancer Survivors
Feasibility Outcomes of a Pilot Randomized Clinical Trial to Increase Cruciferous and Green Leafy Vegetable Intake in Posttreatment Head and Neck Cancer Survivors Open
View article: Epigenetic Regulation of Metabolism and Inflammation by Calorie Restriction
Epigenetic Regulation of Metabolism and Inflammation by Calorie Restriction Open
View article: Computational methods to identify bimodal gene expression and facilitate personalized treatment in cancer patients
Computational methods to identify bimodal gene expression and facilitate personalized treatment in cancer patients Open
Standard methods for detecting cancer-associated genes rely on comparison of sample means between cancer patients and healthy controls. While such methods have successfully identified several oncogenes and tumor suppressor genes, they negl…
View article: Chronic social stress induces DNA methylation changes at an evolutionary conserved intergenic region in chromosome X
Chronic social stress induces DNA methylation changes at an evolutionary conserved intergenic region in chromosome X Open
Chronic stress resulting from prolonged exposure to negative life events increases the risk of mood and anxiety disorders. Although chronic stress can change gene expression relevant for behavior, molecular regulators of this change have n…
View article: Chronic social stress induces DNA methylation changes at an evolutionary conserved intergenic region in chromosome X
Chronic social stress induces DNA methylation changes at an evolutionary conserved intergenic region in chromosome X Open
Chronic stress resulting from prolonged exposure to negative life events increases the risk of mood and anxiety disorders. Although chronic stress can change gene expression relevant for behavior, molecular regulators of this change have n…
View article: Early-Life Nutritional Programming of Cognition—The Fundamental Role of Epigenetic Mechanisms in Mediating the Relation between Early-Life Environment and Learning and Memory Process
Early-Life Nutritional Programming of Cognition—The Fundamental Role of Epigenetic Mechanisms in Mediating the Relation between Early-Life Environment and Learning and Memory Process Open
View article: Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure
Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure Open
Chronic exposure to glucocorticoids (GCs) can lead to psychiatric complications through epigenetic mechanisms such as DNA methylation (DNAm). We sought to determine whether epigenetic changes in a peripheral tissue can serve as a surrogate…
View article: Failure to upregulate Agrp and Orexin in response to activity based anorexia in weight loss vulnerable rats characterized by passive stress coping and prenatal stress experience
Failure to upregulate Agrp and Orexin in response to activity based anorexia in weight loss vulnerable rats characterized by passive stress coping and prenatal stress experience Open