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A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made theExpand
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Gene Expression–Based Recurrence Prediction of Hepatitis B Virus–Related Human Hepatocellular Carcinoma
Purpose: The poor prognosis of hepatocellular carcinoma (HCC) is, in part, due to the high rate of recurrence even after “curative resection” of tumors. Therefore, it is axiomatic that theExpand
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Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction
Objective Cancer can involve gene dysregulation via multiple mechanisms, so no single level of genomic data fully elucidates tumor behavior due to the presence of numerous genomic variations withinExpand
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Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects
Background and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to beExpand
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Difference-based clustering of short time-course microarray data with replicates
  • J. Kim, J. Kim
  • Computer Science, Medicine
  • BMC Bioinformatics
  • 14 July 2007
BackgroundThere are some limitations associated with conventional clustering methods for short time-course gene expression data. The current algorithms require prior domain knowledge and do notExpand
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Genomic evidence of reactive oxygen species elevation in papillary thyroid carcinoma with Hashimoto thyroiditis.
Elevated levels of reactive oxygen species (ROS) have been proposed as a risk factor for the development of papillary thyroid carcinoma (PTC) in patients with Hashimoto thyroiditis (HT). However, itExpand
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Histone deacetylase regulates high mobility group A2-targeting microRNAs in human cord blood-derived multipotent stem cell aging
Cellular senescence involves a reduction in adult stem cell self-renewal, and epigenetic regulation of gene expression is one of the main underlying mechanisms. Here, we observed that the cellularExpand
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Synergistic effect of different levels of genomic data for cancer clinical outcome prediction
There have been many attempts in cancer clinical-type classification by using a dataset from a number of molecular layers of biological system. Despite these efforts, however, it still remainsExpand
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ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizingExpand
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Identifying set-wise differential co-expression in gene expression microarray data
BackgroundPrevious differential coexpression analyses focused on identification of differentially coexpressed gene pairs, revealing many insightful biological hypotheses. However, this method couldExpand
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