Ming-Kun Chen 0 Wen-Ping Hsieh 0 Chang-Hsien Yang 0 0 Graduate Institute of Biotechnology, National Chung Hsing University , Taichung, Taiwan 40227 ROC Two lily (Lilium longiflorum) PISTILLATA (PI
Background Normalization of gene expression data has been studied for many years and various strategies have been formulated to deal with various types of data. Most normalization algorithms rely on the assumption that the number of up-regulated genes and the number of down-regulated genes are roughly the same. However, the well-known Golden Spike experiment presents a unique...
Copy number variation (CNV) has been reported to be associated with disease and various cancers. Hence, identifying the accurate position and the type of CNV is currently a critical issue. There are many tools targeting on detecting CNV regions, constructing haplotype phases on CNV regions, or estimating the numerical copy numbers. However, none of them can do all of the three...
Chuang 5 Chung-Yu Lan 4 Wen-Ping Hsieh 3 Bor-Sen Chen 0 0 Department of Electrical Engineering, National Tsing Hua University , Hsinchu 30013 , Taiwan 1 Institute of Communication Engineering, National
Background Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of approaches have been used to predict gene functions and...
Yu-Chao Wang 0 Che Lin Ming-Ta Chuang 0 Wen-Ping Hsieh Chung-Yu Lan Yung-Jen Chuang Bor-Sen Chen 0 0 Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing
MicroRNAs (miRNAs) have a major impact on regulatory networks in human carcinogenesis. In this study, we sought to investigate the prognostic significance of miRNAs in patients with oral cavity squamous cell carcinoma (OSCC). In a discovery phase, RNA was extracted from 58 OSCC tumor samples and paired normal tissues. MiRNAs expression was evaluated with TaqMan Array Card and...
, Chun-Cheih Chao , Fu-Chen Liu , Po-Chen Hsu , Hsueh-Fen Chen , Shih-Chi Peng , Yung-Jen Chuang , Chung-Yu Lan , Wen-Ping Hsieh , David Shan Hill Wong: Dynamic Transcript Profiling of Candida albicans ... : D535 - 539 . 16. Yu-Chao Wang , Che Lin , Ming-Ta Chuang , Wen-Ping Hsieh , Chung-Yu Lan , Yung-Jen Chuang , Bor-Sen Chen : Interspecies protein interaction network construction for characterization of
Deciphering the causal networks of gene interactions is critical for identifying disease pathways and disease-causing genes. We introduce a method to reconstruct causal networks based on exploring phenotype-specific modules in the human interactome and including the expression quantitative trait loci (eQTLs) that underlie the joint expression variation of each module. Closely...
Background Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore...
Background Candida albicans is a commonly encountered fungal pathogen in humans. The formation of biofilm is a major virulence factor in C. albicans pathogenesis and is related to antidrug resistance of this organism. Although many factors affecting biofilm have been analyzed, molecular mechanisms that regulate biofilm formation still await to be elucidated. Results In this study...
Candida albicans is responsible for a number of life-threatening infections and causes considerable morbidity and mortality in immunocompromised patients. Previous studies of C. albicans pathogenesis have suggested several steps must occur before virulent infection, including early adhesion, invasion, and late tissue damage. However, the mechanism that triggers C. albicans...
BackgroundInherited cardiac conduction diseases (CCD) are rare but are caused by mutations in a myriad of genes. Recently, whole-exome sequencing has successfully led to the identification of causal mutations for rare monogenic Mendelian diseases. ObjectiveTo investigate the genetic background of a family affected by inherited CCD. Methods and ResultsWe used whole-exome...
Background SUMOylation, as part of the epigenetic regulation of transcription, has been intensively studied in lower eukaryotes that contain only a single SUMO protein; however, the functions of SUMOylation during mammalian epigenetic transcriptional regulation are largely uncharacterized. Mammals express three major SUMO paralogues: SUMO-1, SUMO-2, and SUMO-3 (normally referred...
Molecular methods for predicting prognosis in patients with oral cavity squamous cell carcinoma (OSCC) are urgently needed, considering its high recurrence rate and tendency for metastasis. The present study investigated the genetic basis of variations in gene expression associated with poor prognosis in OSCC using Affymetrix SNP 6.0 and Affymetrix GeneChip Human Gene 1.0 ST...
Background Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing microarrays, Affymetrix Porcine, Affymetrix Human U133+2.0, and the U.S. Pig Genome Coordination Program spotted glass oligonucleotide microarrays were compared for their reproducibility, coverage, platform...