SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis

SNPAnalyzer is a software that performs four essential statistical analyses of SNPs in a common computational environment. It is composed of three main modules: (i) data manipulation, (ii) analysis and (iii) visualization. The data manipulation module is responsible for data input and output, and handles genotype, phenotype and genetic distance data. To ensure user convenience, the data format is simple. The analysis module performs statistical calculations and consists of four subcomponents: (i) Hardy–Weinberg equilibrium, (ii) Haplotype Estimation, (iii) linkage disequilibrium (LD) and (iv) quantitative trait locus analysis. The main feature of the analysis module is multiple implementations of different algorithms and indices for haplotype estimation and for LD analysis. This enables users to compare separate results generated by different algorithms, which help to avoid biased results acquired by applying a single statistical algorithm. The performance of all implemented algorithms has been validated using experimentally proven datasets. The visualization module presents most of the analyzed results as figures, rather than as simple text, which aids in the intuitive understanding of complex data. The SNPAnalyzer has been developed using C and C++ and is available at

CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome

<p>Abstract</p> <p>Background</p> <p>Genomic alterations frequently occur in many cancer patients and play important mechanistic roles in the pathogenesis of cancer. Furthermore, they can modify the expression level of genes due to altered copy number in the corresponding region of the chromosome. An accumulating body of evidence supports the possibility that strong genome-wide correlation exists between DNA content and gene expression. Therefore, more comprehensive analysis is needed to quantify the relationship between genomic alteration and gene expression. A well-designed bioinformatics tool is essential to perform this kind of integrative analysis. A few programs have already been introduced for integrative analysis. However, there are many limitations in their performance of comprehensive integrated analysis using published software because of limitations in implemented algorithms and visualization modules.</p> <p>Results</p> <p>To address this issue, we have implemented the Java-based program CHESS to allow integrative analysis of two experimental data sets: genomic alteration and genome-wide expression profile. CHESS is composed of a genomic alteration analysis module and an integrative analysis module. The genomic alteration analysis module detects genomic alteration by applying a threshold based method or SW-ARRAY algorithm and investigates whether the detected alteration is phenotype specific or not. On the other hand, the integrative analysis module measures the genomic alteration's influence on gene expression. It is divided into two separate parts. The first part calculates overall correlation between comparative genomic hybridization ratio and gene expression level by applying following three statistical methods: simple linear regression, Spearman rank correlation and Pearson's correlation. In the second part, CHESS detects the genes that are differentially expressed according to the genomic alteration pattern with three alternative statistical approaches: Student's t-test, Fisher's exact test and Chi square test. By successive operations of two modules, users can clarify how gene expression levels are affected by the phenotype specific genomic alterations. As CHESS was developed in both Java application and web environments, it can be run on a web browser or a local machine. It also supports all experimental platforms if a properly formatted text file is provided to include the chromosomal position of probes and their gene identifiers.</p> <p>Conclusions</p> <p>CHESS is a user-friendly tool for investigating disease specific genomic alterations and quantitative relationships between those genomic alterations and genome-wide gene expression profiling.</p

SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis

<p>Abstract</p> <p>Background</p> <p>Since the completion of the HapMap project, huge numbers of individual genotypes have been generated from many kinds of laboratories. The efforts of finding or interpreting genetic association between disease and SNPs/haplotypes have been on-going widely. So, the necessity of the capability to analyze huge data and diverse interpretation of the results are growing rapidly.</p> <p>Results</p> <p>We have developed an advanced tool to perform linkage disequilibrium analysis, and genetic association analysis between disease and SNPs/haplotypes in an integrated web interface. It comprises of four main analysis modules: (i) data import and preprocessing, (ii) haplotype estimation, (iii) LD blocking and (iv) association analysis. Hardy-Weinberg Equilibrium test is implemented for each SNPs in the data preprocessing. Haplotypes are reconstructed from unphased diploid genotype data, and linkage disequilibrium between pairwise SNPs is computed and represented by D', r²and LOD score. Tagging SNPs are determined by using the square of Pearson's correlation coefficient (r²). If genotypes from two different sample groups are available, diverse genetic association analyses are implemented using additive, codominant, dominant and recessive models. Multiple verified algorithms and statistics are implemented in parallel for the reliability of the analysis.</p> <p>Conclusion</p> <p>SNPAnalyzer 2.0 performs linkage disequilibrium analysis and genetic association analysis in an integrated web interface using multiple verified algorithms and statistics. Diverse analysis methods, capability of handling huge data and visual comparison of analysis results are very comprehensive and easy-to-use.</p

Mature cystic teratoma of the pancreas: A rare cystic neoplasm

Mature cystic teratoma of the pancreas is an extremely rare benign neoplasm. Only 51 cases have been reported in the literature. Its cystic nature often appears to have malignant potential in preoperative image studies. Moreover, no characteristic features could be shown on image studies, such as abdominal CT scan or pancreas MRI. The accurate diagnosis is generally obtained after surgical resection. We present a rare case of a 53-year-old male with mature cystic teratoma of the pancreas, which was confirmed on pathology after laparoscopic distal pancreatectomy

Biological age as a useful index to predict seventeen-year survival and mortality in Koreans

Abstract Background Many studies have been conducted to quantitatively estimate biological age using measurable biomarkers. Biological age should function as a valid proxy for aging, which is closely related with future work ability, frailty, physical fitness, and/or mortality. A validation study using cohort data found biological age to be a superior index for disease-related mortality than chronological age. The purpose of this study is to demonstrate the validity of biological age as a useful index to predict a person\u2019s risk of death in the future. Methods The data consists of 13,106 cases of death from 557,940 Koreans at 20\u201393 years old, surveyed from 1994 to 2011. Biological ages were computed using 15 biomarkers measured in general health check-ups using an algorithm based on principal component analysis. The influence of biological age on future mortality was analyzed using Cox proportional hazards regression considering gender, chronological age, and event type. Results In the living subjects, the average biological age was almost the same as the average chronological age. In the deceased, the biological age was larger than the chronological age: largest increment of biological age over chronological age was observed when their baseline chronological age was within 50\u201359 years. The death rate significantly increased as biological age became larger than chronological age (linear trend test, p value\u2009<\u20090.0001). The largest hazard ratio was observed in subjects whose baseline chronological age was within 50\u201359 years when the cause was death from non-cancerous diseases (HR\u2009=\u20091.30, 95% confidence intervals\u2009=\u20091.26 - 1.34). The survival probability, over the 17\ua0year term of the study, was significantly decreased in the people whose biological age was larger than chronological age (log rank test, p value\u2009<\u20090.001). Conclusions Biological age could be used to predict future risk of death, and its effect size varied according to gender, chronological age, and cause of death

Transport characteristics of wastewater effluent organic matter in nanofiltration and ultrafiltration membranes

This study demonstrates the transport characteristics of wastewater effluent organic matter (EfOM) through membrane pores using a four-parameter (intrinsic mass transfer coefficient (k(i)), solute) concentration near the membrane surface (C-m) solute permeability (P-m), and reflection coefficient (sigma) model based on thermodynamics, concentration polarization (CP) and hydrodynamic operating conditions represented by a J(o)/k ratio (the ratio of initial permeate flux (J(o)) to a back diffusional mass transfer coefficient (k)). EfOM transport characteristics through the pores of four different membranes (a nanofiltration (NF)/ultrafiltration (UF) polymeric pair and two ceramic UF membranes with different molecular weight cutoffs (MWCOs)) were different; the NF polymeric membrane exhibited either convection- or diffusion-dominant conditions, while the UF membranes exhibited convection-dominant conditions in terms of EfOM transport through membrane pores. A critical J(o)/k ratio (representing a transitional condition between diffusion- and convection-dominant transport of solute) was found for the examined NF membrane with a MWCO of 250 Daltons. Four different parameters (k(i), C-m, P-m, and sigma) were determined by the model to be informative to elucidate the various interactions between EfOM and the tested membranes. EfOM characteristics (size, structure, and functionality) and membrane properties (MWCO, surface/pore charge in terms of zeta potential, and module configurations) were revealed to play a major role in EfOM rejection and flux decline under convection-dominant conditions, as compared to diffusion-dominant conditionsopen3

The Suppressive Effects of Cinnamomi Cortex and Its Phytocompound Coumarin on Oxaliplatin-Induced Neuropathic Cold Allodynia in Rats

Oxaliplatin, a chemotherapy drug, induces acute peripheral neuropathy characterized by cold allodynia, spinal glial activation and increased levels of pro-inflammatory cytokines. Herein, we determined whether Cinnamomi Cortex (C. Cortex), a widely used medicinal herb in East Asia for cold-related diseases, could attenuate oxaliplatin-induced cold allodynia in rats and the mechanisms involved. A single oxaliplatin injection (6 mg/kg, i.p.) induced significant cold allodynia signs based on tail immersion tests using cold water (4 °C). Daily oral administration of water extract of C. Cortex (WECC) (100, 200, and 400 mg/kg) for five consecutive days following an oxaliplatin injection dose-dependently alleviated cold allodynia with only a slight difference in efficacies between the middle dose at 200 mg/kg and the highest dose at 400 mg/kg. WECC at 200 mg/kg significantly suppressed the activation of astrocytes and microglia and decreased the expression levels of IL-1β and TNF in the spinal cord after injection with oxaliplatin. Furthermore, oral administration of coumarin (10 mg/kg), a major phytocompound of C. Cortex, markedly reduced cold allodynia. These results indicate that C. Cortex has a potent anti-allodynic effect in oxaliplatin-injected rats through inhibiting spinal glial cells and pro-inflammatory cytokines. We also suggest that coumarin might play a role in the anti-allodynic effect of C. Cortex

Constructing a Knowledge-Based Database for Dermatological Integrative Medical Information

Recently, overuse of steroids and immunosuppressive drugs has produced incurable dermatological health problems. Traditional medical approaches have been studied for alternative solutions. However, accessing relevant information is difficult given the differences in information for western medicine (WM) and traditional medicine (TM). Therefore, an integrated medical information infrastructure must be utilized to bridge western and traditional treatments. In this study, WM and TM information was collected based on literature searches and information from internet databases on dermatological issues. Additionally, definitions for unified terminology and disease categorization based on individual cases were generated. Also a searchable database system was established that may be a possible model system for integrating both WM and TM medical information on dermatological conditions. Such a system will yield benefits for researchers and facilitate the best possible medical solutions for patients. The DIMI is freely available online

SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis-7

Nberg Equilibrium test are shown in the table. Triggering tabs for Data Import, Haplotype Estimation, LD Blocking and Case-Control Study are shown on the left panel.<p><b>Copyright information:</b></p><p>Taken from "SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis"</p><p>http://www.biomedcentral.com/1471-2105/9/290</p><p>BMC Bioinformatics 2008;9():290-290.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2453143.</p><p></p