• Interdisciplinary Bio Central
• /
• v.5 no.1
• /
• pp.1.1-1.8
• /
• 2013

High quality publicly-available transcriptomic data representing relationships in gene expression across a diverse set of biological conditions is used as a context network to explore transcriptomics of the CNS. The context network, 18367Hu-matrix, contains pairwise Pearson correlations for 22,215 human genes across18,637 human tissue samples1. To do this, we compute a network derived from biological samples from CNS cells and tissues, calculate clusters of co-expressed genes from this network, and compare the significance of these to clusters derived from the larger 18367Hu-matrix network. Sorting and visualization uses the publicly available software, MetaOmGraph (http://www.metnetdb.org/MetNet_MetaOm-Graph.htm). This identifies genes that characterize particular disease conditions. Specifically, differences in gene expression within and between two designations of glial cancer, astrocytoma and glioblastoma, are evaluated in the context of the broader network. Such gene groups, which we term outlier-networks, tease out abnormally expressed genes and the samples in which this expression occurs. This approach distinguishes 48 subnetworks of outlier genes associated with astrocytoma and glioblastoma. As a case study, we investigate the relationships among the genes of a small astrocytoma-only subnetwork. This astrocytoma-only subnetwork consists of SVEP1, IGF1, CHRNA3, and SPAG6. All of these genes are highly coexpressed in a single sample of anaplastic astrocytoma tumor (grade III) and a sample of juvenile pilocytic astrocytoma. Three of these genes are also associated with nicotine. This data lead us to formulate a testable hypothesis that this astrocytoma outlier-network provides a link between some gliomas/astrocytomas and nicotine.

• Molecules and Cells
• /
• v.42 no.3
• /
• pp.237-244
• /
• 2019

Understanding the mechanisms of cancer drug resistance is a critical challenge in cancer therapy. For many cancer drugs, various resistance mechanisms have been identified such as target alteration, alternative signaling pathways, epithelial-mesenchymal transition, and epigenetic modulation. Resistance may arise via multiple mechanisms even for a single drug, making it necessary to investigate multiple independent models for comprehensive understanding and therapeutic application. In particular, we hypothesize that different resistance processes result in distinct gene expression changes. Here, we present a web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance. Resistance signatures were extracted from two different types of datasets. First, resistance signatures were extracted from transcriptomic profiles of cancer cells or patient samples and their resistance-induced counterparts for >30 cancer drugs. Second, drug resistance group signatures were also extracted from two large-scale drug sensitivity datasets representing ~1,000 cancer cell lines. All the datasets are available for download, and are conveniently accessible based on drug class and cancer type, along with analytic features such as clustering analysis, multidimensional scaling, and pathway analysis. CDRgator allows meta-analysis of independent resistance models for more comprehensive understanding of drug-resistance mechanisms that is difficult to accomplish with individual datasets alone (database URL: http://cdrgator.ewha.ac.kr).

• The Journal of the Korea Contents Association
• /
• v.14 no.1
• /
• pp.528-536
• /
• 2014

The purpose of this study was to examine the effectiveness of drama education program for elementary school students by using method of meta-analysis. For the purpose of the study, master's theses, doctoral dissertations, and journal articles published in Korea up to July, 2013 were systematically reviewed. As a result, a total of 19 studies were eligible for the inclusion criteria. The mean effect sizes and test for homogeneity of effect size(Q-statistic) were analyzed by using Comprehensive Meta-Analysis software 2.0. The main findings of the study were as follows. First, the average effect sizes for drama education program were ES=1.103 of self-expression, ES=1.011 of self-esteem, ES= .858 of creativity and ES= .672 of sociality. Second, by analysing the moderate variables of the effect size for drama education program, 'sessions' were statistically significant. Based on the study results, the research and practice implications were discussed.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.11
• /
• pp.4759-4768
• /
• 2015

Background: Several studies have investigated predictive and prognostic biomarkers for patients treated with anti-epidermal growth factor receptor (EGFR) agents in lung cancer. However, the conclusion is controversial. Materials and Methods: A meta-analysis was conducted to evaluate the associations of mutant K-ras, PIK3CA and PTEN deficiency with the efficacy of anti-EGFR agents in lung cancer. The primary endpoint was objective response rate (ORR). The secondary endpoints were overall survival (OS) and progression-free survival (PFS). Results: A total of 61 studies were included in the final meta-analysis. The result showed that K-ras mutation was a good predictor for ORR (RR=0.42, 95%CI, 0.33-0.55, p=0.000) and an effective prognostic marker for OS (HR=1.37, 95%CI, 1.15-1.65, p=0.001) and PFS (HR=1.33, 95%CI, 1.05-1.69, p=0.019). However, PTEN deficiency or PIK3CA mutation did not show any significance predictive value for ORR (PTEN, RR=0.82, 95%CI, 0.56-1.19, p=0.286; PIK3CA, RR=1.08, 95%CI, 0.17-6.66, P=0.938). And PTEN deficiency or expression of PIK3CA did not show significance prognostic value for OS (PTEN, HR=0.88, 95%CI, 0.31-2.46,P=0.805; PIK3CA, HR=0.79, 95%CI: 0.23-2.68, P=0.706). Conclusions: Our meta-analysis showed that K-ras mutation may be an effective predictor in lung cancer patients treated with anti-EGFR agents. Whereas, the predictive and prognostic value of PTEN deficiency and PIK3CA mutation need to be further investigated.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.18
• /
• pp.7583-7588
• /
• 2014

Background: Colorectal cancer (CRC) is a major cause of cancer-related death and cancer-related incidence worldwide. The potential of microRNA-21 (miR-21) as a biomarker for CRC detection has been studied in several studies. However, the results were inconsistent. Therefore, we conducted the present meta-analysis to systematically assess the diagnostic value of miR-21 for CRC. Materials and Methods: Using a random-effect model, the pooled sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) were calculated to evaluate the diagnostic performance of miR-21 for CRC. A summary receiver operating characteristic (SROC) curve and an area under the curve (AUC) were also generated to assess the diagnosis accuracy of miR-21 for CRC. Q test and I2 statistics were used to assess between-study heterogeneity. Publication bias was evaluated by the Deeks' funnel plot asymmetry test. Results: A total of 986 CRC patients and 702 matched healthy controls from 8 studies were involved in the meta-analysis. The pooled results for SEN, SPE, PLR, NLR, DOR, and AUC were 57% (95%CI: 39%-74%), 87% (95%CI: 78%-93%), 4.4 (95%CI: 2.4-8.0), 0.49 (95%CI: 0.32-0.74), 9 (95%CI: 4-22), and 0.83 (95%CI: 0.79-0.86), respectively. Subgroup analyses further suggested that blood-based studies showed a better diagnostic accuracy compared with feces-based studies, indicating that blood may be a better matrix for miR-21 assay and CRC detection. Conclusions: Our findings suggest that miR-21 has a potential diagnostic value for CRC with a moderate level of overall diagnostic accuracy. Hence, it could be used as auxiliary means for the initial screening of CRC and avoid unnecessary colonoscopy, which is an invasive and expensive procedure.

• The Journal of Korean Institute of Communications and Information Sciences
• /
• v.30 no.8B
• /
• pp.549-561
• /
• 2005

As Internet and network technologies have been developed, e-commerces are getting more complex and more various. This paper, for meta-data and data exchange between heterogeneous database systems, uses XML schema proposed in W3C, and XML schema can present meta-data and data of relational database system as XML document format which is structural. It supports various primitive data formats, so that it uses the structure which reflects adequately data formats which relational database system offered. However, current e-commerces use heterogeneous platforms, so difficulties that is mutual interchange and management exist. For the solution for these problems, a standard ontology which defines relations of product classifications and the standard of property expression and the location ontology which offers e-commerce's information about products are constructed. Applying these ontology information to search system, by offering information which customers need efficient search is performed. Combining these ontologies and product classification category information, called XMDR, this XMDR is introduced into product search system, so this paper proposes to construct ontology server method for efficient search.

• Journal of KIISE:Software and Applications
• /
• v.33 no.2
• /
• pp.143-153
• /
• 2006

Microarray which enables us to obtain hundreds and thousands of expression of gene or genotype at once is an epoch-making technology in comparative analysis of genes. First of all, we have to measure the intensity of each gene in an microarray image from the experiment to gain the expression level of each gene. But it is difficult to analyze the microarray image in manual because it has a lot of genes. Meta-gridding method and various auto-gridding methods have been proposed for this, but thew still have some problems. For example, meta-gridding requires manual-work due to some variations in spite of experiment in same microarray, and auto-gridding nay not carried out fully or correctly when an image has a lot of noises or is lowly expressed. In this article, we propose Hierarchical Grid Alignment algorithm for new methodology combining meta-gridding method with auto-gridding method. In our methodology, we necd a meta-grid as an input, and then align it with the microarray image automatically. Experimental results show that the proposed method serves more robust and reliable gridding result than the previous methods. It is also possible for user to do more reliable batch analysis by using our algorithm.

• 한국HCI학회:학술대회논문집
• /
• 2009.02a
• /
• pp.1009-1014
• /
• 2009

Meta-thinking is a kind of thinking beyond certain scope or border, which sees objects as an expanded definition exceeding its essence. It can be experienced when people come into contact with new things. As for digital media, experience acquired from computer screen makes users' thinking be changed continuously and help their thinking to be expanded. Today, studies on development of digital technology regarding virtual reality (VR) and experience obtained from digital media become a topic of conversation, however, this experience depends on the sense of sight through screen. Actually, transparent experiences in digital media are not the same with those in real world, therefore, this study investigated experience expansion through interaction with real things which are much closer to daily lives than virtual experiences. It can be found in media art which induces positive participation of audiences and shows them a new meaning through delight and amusement experienced in the process of interaction. Visual expression in digital media should be more than spectacular which is only full of excessive images. In addition, interface should not be remained as an expression from technological attempts, instead, it is necessary to find humans aspiration with meta-thinking which accepts things expansively and visualize their experiences.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.5
• /
• pp.2329-2334
• /
• 2012

Introduction: Many studies have reported that microRNA-21 (miR-21) mihght predict the survival outcome in non-small cell lung cancers (NSCLCs) but the opposite opinion has also been expressed. The aim of this study was to summarize the evidence for a prognostic role of miR-21. Materials and Methods: All the eligible studies was searched by Medline and EMBASE and patients' clinical characteristics and survival outcome were extracted. Then a meta-analysis was performed to clarify the prognostic role of the miR-21 expression in different subgroups. Results: A total of 8 eligible articles were yielded covering survival outcomes or clinical characteristics. The combined hazard ratio (HR) and 95% confidence interval (95% CI) for overall survival (OS) was 2.19 [0.76, 6.30], while the combined HR (95% CI) of Asian group for OS had a significant result, 5.49 [2.46, 12.27]. The combined HR (95% CI) for recurrence free survival or disease free survival (RFS/DFS) was 2.31 [1.52, 3.49]. Odds ratios (ORs) showed that the miR-21 expression was associated with lymph node status and histological type. Conclusion: miR-21 expression could predict the prognostic outcome of NSCLC in Asians, despite some deficiencies in the study data.

• Proceedings of the Korean Society of Fisheries Technology Conference
• /
• 2000.05a
• /
• pp.161-162
• /
• 2000

Metalloprotease produced in Vibrio mimicus, in which zinc is an essential meta ion for catalytic activity, degrades a variety of biologically important substances including human collagen, several complement components, and immunoglobulin. For gene overexpression and convenient purification, VMC gene was constructed in pET22b(+) expression vector by using of PCR. (omitted)