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RAN-aCGH: R GUI Tools for Analysis and Visualization of an Array-CGH Experiment

Kim S, Kim BS

  • KMID: 2166270
  • Genomics Inform.
  • 2007 Sep;5(3):137-139.
RAN-aCGH is an R GUI tool for the analysis and visualization of array comparative genomic hybridization (array-CGH) experiments. The tool consists of data-loading, preprocessing for missing data, several methods for...
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GSnet: An Integrated Tool for Gene Set Analysis and Visualization

Choi YJ, Woo HG, Yu U

  • KMID: 2166269
  • Genomics Inform.
  • 2007 Sep;5(3):133-136.
The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform....
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arrayImpute: Software for Exploratory Analysis and Imputation of Missing Values for Microarray Data

Lee EK, Yoon D, Park T

  • KMID: 2166268
  • Genomics Inform.
  • 2007 Sep;5(3):129-132.
arrayImpute is a software for exploratory analysis of missing data and imputation of missing values in microarray data. It also provides a comparative analysis of the imputed values obtained from...
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PathTalk: Interpretation of Microarray Gene-Expression Clusters in Association with Biological Pathways

Chung TS, Chung HJ, Kim JH

  • KMID: 2166267
  • Genomics Inform.
  • 2007 Sep;5(3):124-128.
Microarray technology enables us to measure the expression of tens of thousands of genes simultaneously under various experimental conditions. Clustering analysis is one of the most successful methods for analyzing...
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Effect of Normalization on Detection of Differentially-Expressed Genes with Moderate Effects

Cho S, Lee E, Kim Y, Park T

  • KMID: 2166266
  • Genomics Inform.
  • 2007 Sep;5(3):118-123.
The current existing literature offers little guidance on how to decide which method to use to analyze one-channel microarray measurements when dealing with large, grouped samples. Most previous methods have...
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Fluorescence Quenching Causes Systematic Dye Bias in Microarray Experiments Using Cyanine Dye

Jeon H, Choi S

  • KMID: 2166265
  • Genomics Inform.
  • 2007 Sep;5(3):113-117.
The development of microarray technology has facilitated the understanding of gene expression profiles. Despite its convenience, the cause of dye-bias that confounds data interpretation in dual-color DNA microarray experiments is...
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Statistical Analysis of Gene Expression in Innate Immune Responses: Dynamic Interactions between MicroRNA and Signaling Molecules

Piras V, Selvarajoo K, Fujikawa N, Choi S, Tomita M, Giuliani A, Tsuchiya M

  • KMID: 2166264
  • Genomics Inform.
  • 2007 Sep;5(3):107-112.
MicroRNAs (miRNAs) are known to negatively control protein-coding genes by binding to messenger RNA (mRNA) in the cytoplasm. In innate immunity, the role of miRNA gene silencing is largely unknown....
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Prediction of the Exposure to 1763MHz Radiofrequency Radiation Based on Gene Expression Patterns

Lee MS, Huang TQ, Seo JS, Park WY

  • KMID: 2166263
  • Genomics Inform.
  • 2007 Sep;5(3):102-106.
Radiofrequency (RF) radiation at the frequency of mobile phones has been not reported to induce cellular responses in in vitro and in vivo models. We exposed HEI-OC1, conditionally-immortalized mouse auditory...
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An Application of the Clustering Threshold Gradient Descent Regularization Method for Selecting Genes in Predicting the Survival Time of Lung Carcinomas

Lee S, Kim Y

  • KMID: 2166262
  • Genomics Inform.
  • 2007 Sep;5(3):95-101.
In this paper, we consider the variable selection methods in the Cox model when a large number of gene expression levels are involved with survival time. Deciding which genes are...
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