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Article
Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays
We compared different hybridization conditions of oligonucleotide-based DNA microarray to acquire optimized and reliable microarray data. Several parameters were evaluated at different hybridization conditions...
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Article
c-Abl regulates Early Growth Response Protein (EGR1) in response to oxidative stress
c-Abl is a tyrosine kinase that can act as a regulator of cell growth and apoptosis in response to stress. Using cell lines expressing c-Abl in an inducible manner, we identified genes whose expression was reg...
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Article
DNA (cytosine-5)-methyltransferase 1 as a mediator of mutant p53-determined p16ink4A down-regulation
In cancer, gene silencing via hypermethylation is as common as genetic mutations in p53. Understanding the relationship between mutant p53 and hypermethylation of other tumor suppressor genes is essential when el...
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Article
Open AccessA model-based circular binary segmentation algorithm for the analysis of array CGH data
Circular Binary Segmentation (CBS) is a permutation-based algorithm for array Comparative Genomic Hybridization (aCGH) data analysis. CBS accurately segments data by detecting change-points using a maximal-t test...
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Article
Open AccessPrediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population
Breast cancer is a heterogeneous disease in terms of transcriptional aberrations; moreover, microarray gene expression profiles had defined 5 molecular subtypes based on certain intrinsic genes. This study aim...
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Article
Open AccessIdentification of reproducible gene expression signatures in lung adenocarcinoma
Lung cancer is the leading cause of cancer-related death worldwide. Tremendous research efforts have been devoted to improving treatment procedures, but the average five-year overall survival rates are still l...
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Article
Open AccessUtilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome
Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by SCN5A mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated throu...
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Article
Open AccessIdentification of Genes with Consistent Methylation Levels across Different Human Tissues
DNA methylation plays an important role in regulating cell growth and disease development. Methylation profiles are examined by bisulfite conversion; however, the lack of markers for bisulfite conversion effic...
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Article
Open AccessSNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women
Numerous efforts have been made to elucidate the etiology and improve the treatment of lung cancer, but the overall five-year survival rate is still only 15%. Although cigarette smoking is the primary risk fac...
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Article
Open AccessMicroRNA-769-3p Down-regulates NDRG1 and Enhances Apoptosis in MCF-7 Cells During Reoxygenation
Hypoxia and reoxygenation are common characteristics of solid tumors, which lead to oxidative stress and activation of stress-response genes. Previously, we observed that N-myc downstream-regulated gene 1 (NDRG1)...
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Article
Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures
Several prognostic signatures have been identified for breast cancer. However, these signatures vary extensively in their gene compositions, and the poor concordance of the risk groups defined by the prognosti...
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Article
Open AccessIdentification of Gene Expression Biomarkers for Predicting Radiation Exposure
A need for more accurate and reliable radiation dosimetry has become increasingly important due to the possibility of a large-scale radiation emergency resulting from terrorism or nuclear accidents. Although t...
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Article
Open AccessDisease-Targeted Sequencing of Ion Channel Genes identifies de novo mutations in Patients with Non-Familial Brugada Syndrome
Brugada syndrome (BrS) is one of the ion channelopathies associated with sudden cardiac death (SCD). The most common BrS-associated gene (SCN5A) only accounts for approximately 20–25% of BrS patients. This study ...
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Article
Open AccessDeregulated microRNAs in triple-negative breast cancer revealed by deep sequencing
MicroRNAs (miRNAs) are short, non-coding RNA molecules that play critical roles in human malignancy. However, the regulatory characteristics of miRNAs in triple-negative breast cancer, a phenotype of breast ca...
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Article
Open AccessIdentification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma
Although much research effort has been devoted to elucidating lung cancer, the molecular mechanism of tumorigenesis still remains unclear. A major challenge to improve the understanding of lung cancer is the d...
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Article
Open AccessParameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers
In addition to direct targeting and repressing mRNAs, recent studies reported that microRNAs (miRNAs) can bridge up an alternative layer of post-transcriptional gene regulatory networks. The competing endogeno...
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Article
Open AccessCirculating mRNA Profiling in Esophageal Squamous Cell Carcinoma Identifies FAM84B As A Biomarker In Predicting Pathological Response to Neoadjuvant Chemoradiation
Esophageal cancer patients with pathological complete response (pCR) to neoadjuvant chemoradiation (CRT) have favorable outcomes. Currently, there was no reliable biomarker predicting the response to CRT. Peri...
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Article
Open AccessCo-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes
Gene regulation is dynamic across cellular conditions and disease subtypes. From the aspect of regulation under modulation, regulation strength between a pair of genes can be modulated by (dependent on) expres...
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Article
Open AccessGenome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation
Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Previous genome-wide association studies had identified single-nucleotide polymorphisms in several genomic regions to be associated wit...
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Article
Open AccessAryl Hydrocarbon Receptor Activates NDRG1 Transcription under Hypoxia in Breast Cancer Cells
Hypoxia has been intensively investigated over the past several decades based on the observations that hypoxic tumors are more resistant to therapy and have a worse prognosis. Previously, we reported that N-my...
