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Functional analysis reveals the possible role of the C-terminal sequences and PI motif in the function of lily (Lilium longiflorum) PISTILLATA (PI) orthologues

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

The role of TGF-? signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach

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

HaplotypeCN: Copy Number Haplotype Inference with Hidden Markov Model and Localized Haplotype Clustering

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...

Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection

, 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

MicroRNAs MiR-218, MiR-125b, and Let-7g Predict Prognosis in Patients with Oral Cavity Squamous Cell Carcinoma

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...

Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study

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

Causal inference of gene regulation with subnetwork assembly from genetical genomics data

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...

Kernel density weighted loess normalization improves the performance of detection within asymmetrical data

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...

A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle

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...

Dynamic Transcript Profiling of Candida albicans Infection in Zebrafish: A Pathogen-Host Interaction 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...

Whole-Exome Sequencing to Identify a Novel LMNA Gene Mutation Associated with Inherited Cardiac Conduction Disease

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...

Global screening of potential Candida albicans biofilm-related transcription factors via network comparison

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...

Mixture modeling of transcript abundance classes in natural populations

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...

The chromatin modification by SUMO-2/3 but not SUMO-1 prevents the epigenetic activation of key immune-related genes during Kaposi’s sarcoma associated herpesvirus reactivation

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...

A Novel Molecular Signature Identified by Systems Genetics Approach Predicts Prognosis in Oral Squamous Cell Carcinoma

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...

Detection of transcriptional difference of porcine imprinted genes using different microarray platforms

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...