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Search Results: 1 - 10 of 1303 matches for " Yutaka Fukuoka "
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Lower expression of genes near microRNA in C. elegans germline
Hidenori Inaoka, Yutaka Fukuoka, Isaac S Kohane
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-112
Abstract: We analyzed gene expression levels around the 84 of 113 know miRNAs for which there are nearby gene that were measured in the data in two independent C. elegans expression data sets. The expression levels are lower for genes in the vicinity of 59 of 84 (71%) miRNAs as compared to genes far from such miRNAs. Analysis of the genes with lower expression in proximity to the miRNAs reveals increased frequency matching of the 7 nucleotide "seed"s of these miRNAs.We found decreased messenger RNA (mRNA) abundance, localized within a 10 kb of chromosomal distance of some miRNAs, in C. elegans germline. The increased frequency of seed matching near miRNA can explain, in part, the localized effects.MicroRNAs (miRNAs) are short (~22 nt-long) non-protein-coding RNAs. In metazoans, miRNA initially thought to be primarily involved in post-transcriptional control [1] have now been shown to have profound and tissue-specific effects on mRNA transcript abundance across significant fractions of the transcriptome [2]. Concurrently it has been demonstrated that miRNAs have a central role in development and organogenesis [3,4]. In the context of the apparent interactions between miRNA and transcriptional control and mounting evidence for the localized component of transcriptional control [5,6], we performed a genome-wide study of C. elegans to determine a) if there were localized effects of miRNA on transcription and b) if previously identified "seed matching" between miRNA and their gene targets could explain, in part, the observed decrease in expression around some miRNAs.First, the 113 known miRNAs in C. elegans were mapped to the worm genome and genes near each miRNAs were sought. Ninety-six miRNAs were found with at least one gene within 10 kb and 31 miRNA were found within the introns of protein-coding genes. Detailed information about the miRNAs is found in supplemental data. Two experiments of genome-wide expression profiling in C. elegans were analyzed. The first dataset by Kim e
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes
Yutaka Fukuoka, Hidenori Inaoka, Isaac S Kohane
BMC Genomics , 2004, DOI: 10.1186/1471-2164-5-4
Abstract: We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes.We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.As a consequence of DNA sequencing activities, whole-genome sequences for many microbial organisms as well as eukaryotic species are available in publicly accessible databases. DNA microarray technology makes it possible to simultaneously monitor expression patterns of thousand of genes. Expression profiles combined with whole-genome information, especially map information, enable us to investigate a relationship between co-expression of genes and a chromosomal distance (CD).In the pioneering work in this field, Cohen et al. (2000) and Kruglyak and Tang (2000) independently showed that in yeast (Saccharomyces cerevisiae), adjacent pairs of genes show correlated expression [1,2]. In the nematode worm (Caenorhabditis elegans), a study of the relationship between physical distance and expression similarity found many co-expressed pairs of neighboring genes within a distance range of 20 kbp [3]. Clustering of co-expressed genes has been found in humans (Homo sapiens) [4], worm [5] and
A two-step drug repositioning method based on a protein-protein interaction network of genes shared by two diseases and the similarity of drugs
Yutaka Fukuoka,Daiki Takei,Hisamichi Ogawa
Bioinformation , 2013,
Abstract: The present study proposed a two-step drug repositioning method based on a protein-protein interaction (PPI) network of two diseases and the similarity of the drugs prescribed for one of the two. In the proposed method, first, lists of disease related genes were obtained from a meta-database called Genotator. Then genes shared by a pair of diseases were sought. At the first step of the method, if a drug having its target(s) in the PPI network, the drug was deemed a repositioning candidate. Because targets of many drugs are still unknown, the similarities between the prescribed drugs for a specific disease were used to infer repositioning candidates at the second step. As a first attempt, we applied the proposed method to four different types of diseases: hypertension, diabetes mellitus, Crohn disease, and autism. Some repositioning candidates were found both at the first and second steps.
Adaptive thresholds to detect differentially expressed genes in microarray data
Yutaka Fukuoka*,Hidenori Inaoka,Makoto Noshiro
Bioinformation , 2011,
Abstract: To detect changes in gene expression data from microarrays, a fixed threshold for fold difference is used widely. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for lowly expressed genes. In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method.
Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile
Ken Miyaguchi,Yutaka Fukuoka,Mahmut Yasen,Shota Nemoto
Bioinformation , 2011,
Abstract: Microarray analysis has been applied to comprehensively reveal the abnormalities of DNA copy number (CN) and gene expression in human cancer research during the last decade. These analyses have individually contributed to identify the genes associated with carcinogenesis, progression, metastasis of tumor cells and poor prognosis of cancer patients. However, it is known that the correlation between profiles of CN and gene expression does not highly correlate. Factors which determine the degree of correlation remain largely unexplained. To investigate one such factor, we performed trend analyses between the lengths of CN segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC although there was no correlation between the length of CN loss segments and gene expression in CRC. Our findings suggest that the influence of CN on gene expression highly depends on the length of CN region, especially in the case of CN gain. To the best of our knowledge, this is the first study describing the correlation between lengths of CNA segments and expression profiles of corresponding genes.
Systems analysis of inflammatory bowel disease based on comprehensive gene information
Satoru Suzuki, Takako Takai-Igarashi, Yutaka Fukuoka, Dennis P Wall, Hiroshi Tanaka, Peter J Tonellato
BMC Medical Genetics , 2012, DOI: 10.1186/1471-2350-13-25
Abstract: Based on drug indications for IBD, we determined sibling diseases of mild and severe states of IBD. Approximately 1,000 genes associated with the sibling diseases were retrieved from four databases. After ranking the genes by the frequency of records in the databases, we obtained 250 and 253 genes highly associated with the mild and severe IBD states, respectively. We then calculated functional similarities of these genes with known drug targets and examined and presented their interactions as PPI networks.The results demonstrate that this knowledge-based systems approach, predicated on functionally similar genes important to sibling diseases is an effective method to identify important components of the IBD human disease network. Our approach elucidates a previously unknown biological distinction between mild and severe IBD states.Inflammatory Bowel Disease (IBD) is a chronic disease of unknown etiology that causes inflammation and ulcer in intestinal mucosa. Although IBD is still much less prevalent in Japan than in Western countries, the number of Japanese IBD patients has rapidly increased in the last 20 years [1]. This rising trend, also observed in the Asia-Pacific region [2,3] indicates that IBD is rapidly becoming a world-wide disease. There are two major sub-categories of IBD: Crohn's disease (CD) and ulcerative colitis (UC) [4]. Although the pathogenesis of IBD is not fully explained, genetic factors are suggested to contribute to dysregulation of intestinal immunity, leading to gastrointestinal injury.A genetic study of IBD was first reported in 1988 as an epidemiological study of CD patients [5]. Genome-wide scanning (GWS) studies have revealed nine IBD susceptibility loci (IBD1-9) [6] and one susceptibility gene (NOD2) [7]. Genome-Wide Association Studies (GWAS) and corresponding meta-analyses identified 71 susceptibility loci for CD [8] and 47 loci for UC [9]. Recently the genetic susceptibility to IBD was comprehensively reviewed in [10]. Another stud
Development of a Compact Wireless Laplacian Electrode Module for Electromyograms and Its Human Interface Applications
Yutaka Fukuoka,Kenji Miyazawa,Hiroki Mori,Manabi Miyagi,Masafumi Nishida,Yasuo Horiuchi,Akira Ichikawa,Hiroshi Hoshino,Makoto Noshiro,Akinori Ueno
Sensors , 2013, DOI: 10.3390/s130202368
Abstract: In this study, we developed a compact wireless Laplacian electrode module for electromyograms (EMGs). One of the advantages of the Laplacian electrode configuration is that EMGs obtained with it are expected to be sensitive to the firing of the muscle directly beneath the measurement site. The performance of the developed electrode module was investigated in two human interface applications: character-input interface and detection of finger movement during finger Braille typing. In the former application, the electrode module was combined with an EMG-mouse click converter circuit. In the latter, four electrode modules were used for detection of finger movements during finger Braille typing. Investigation on the character-input interface indicated that characters could be input stably by contraction of (a) the masseter, (b) trapezius, (c) anterior tibialis and (d) flexor carpi ulnaris muscles. This wide applicability is desirable when the interface is applied to persons with physical disabilities because the disability differs one to another. The investigation also demonstrated that the electrode module can work properly without any skin preparation. Finger movement detection experiments showed that each finger movement was more clearly detectable when comparing to EMGs recorded with conventional electrodes, suggesting that the Laplacian electrode module is more suitable for detecting the timing of finger movement during typing. This could be because the Laplacian configuration enables us to record EMGs just beneath the electrode. These results demonstrate the advantages of the Laplacian electrode module.
Mollifier Smoothing of tensor fields on differentiable manifolds and applications to Riemannian Geometry
Ryuichi Fukuoka
Mathematics , 2006,
Abstract: Let M be a differentiable manifold. We say that a tensor field g defined on M is non-regular if g is in some local Lp space or if g is continuous. In this work we define a mollifier smoothing g_t of g that has the following feature: If g is a Riemannian metric of class C2, then the Levi-Civita connection and the Riemannian curvature tensor of g_t converges to the Levi-Civita connection and to the Riemannian curvature tensor of g respectively as t converges to zero. Therefore this mollifier smoothing is a good starting point in order to generalize objects of the classical Riemannian geometry to non-regular Riemannian manifolds. Finally we give some applications of this mollifier smoothing. In particular, we generalize the concept of Lipschitz-Killing curvature measure for some non-regular Riemannian manifolds.
Hydrogen bonds are related to the thermal stability of 16S rRNA  [PDF]
Hiroshi Nakashima, Ai Fukuoka, Yuka Saitou
Journal of Biomedical Science and Engineering (JBiSE) , 2013, DOI: 10.4236/jbise.2013.61003

The number of base pairs in the 16S rRNA secondary structures of 51 bacterial sequences was counted, and the number of hydrogen bonds was estimated. The number of hydrogen bonds was highly correlated with the optimal growth temperature (OGT) rather than with the G + C content. Paired and unpaired nucleotides in mesophiles were compared to those in thermophiles. OGT exhibited a relationship with paired nucleotides but not with unpaired nucleotides. The total number of paired as well as unpaired nucleotides in mesophiles was very similar to that in thermophiles. However, the components in base pairs in mesophiles significantly differed from those in thermophiles. As compared with mesophiles, the number of G·C base pairs in thermophiles was high whereas that of A·U base pairs was low. In this study, we showed that hydrogen bonds are important for stabilizing 16S rRNAs at high temperatures.

Is the Tokyo Foreign Exchange Market Efficient from Two Perspectives of Forward Bias and Anomaly?  [PDF]
Yutaka Kurihara
Modern Economy (ME) , 2011, DOI: 10.4236/me.2011.24067
Abstract: This paper examines the efficiency of the Tokyo Foreign Exchange Market from two perspectives. One is whether or not forward bias in this market has existed and the other is the effect of interventions in the market with a focus on whether or not a day-of-the-week anomaly exists in it. Empirical results show that forward exchange rates are a biased predictor of future spot exchange rates; however, there are some anomalies in the market. The findings suggest the conclusion that this market has not been completely efficient.
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