Enhancing performance of gene expression value prediction with cluster-based regression.

BACKGROUND: The inherent correlations among gene expressions have received attention. Recently, it was reported that a set of approximately 1000 landmark genes can be utilized for prediction of expression of other genes (target genes). OBJECTIVE: The objective of this study is to predict expression values of target genes based on expression values of landmark genes. METHODS: A cluster-based regression method is proposed. In the proposed method, clusters are obtained from a set of training instances of a gene and an estimator is obtained per cluster. A test instance is assigned to one of clusters then a regression model corresponding to the cluster predicts expression value. RESULTS: Performance of the proposed method is measured on the GEO (Gene Expression Omnibus) expression data and the GTEx (Genotype-Tissue Expression) expression data. In terms of mean absolute error averaged across target genes, the proposed method significantly outperforms previous approaches in the case of the GEO expression data. CONCLUSIONS: The experimental results report that the combination of clustering and regression can outperform the state-of-the art methods such as generative adversarial networks and a gradient boosting based method.

Performance comparison of dimensionality reduction methods on RNA-Seq data from the GTEx project.

BACKGROUND: One of the apparent characteristics of bioinformatics data is the combination of very large number of features and relatively small number of samples. The vast number of features makes intuitive understanding of a target domain difficult. Dimensionality reduction or manifold learning has potential to circumvent this obstacle, but restricted methods have been preferred. OBJECTIVE: The objective of this study is to observe the characteristics of various dimensionality reduction methods-locally linear embedding (LLE), multi-dimensional scaling (MDS), principal component analysis (PCA), spectral embedding (SE), and t-distributed Stochastic Neighbor Embedding (t-SNE)-on the RNA-Seq dataset from the genotype-tissue expression (GTEx) project. RESULTS: The characteristics of the dimensionality reduction methods are observed on the nine groups of three different tissues in the reduced space with dimensionality of two, three, and four. The visualization results report that each dimensionality reduction method produces a very distinct reduced space. The quantitative results are obtained as the performance of k-means clustering. Clustering in the reduced space from non-linear methods such as LLE, t-SNE and SE achieved better results than in the reduced space produced by linear methods like PCA and MDS. CONCLUSIONS: The experimental results recommend the application of both linear and non-linear dimensionality reduction methods on the target data for grasping the underlying characteristics of the datasets intuitively.

The Effects of Korea Red Ginseng on Inflammatory Cytokines and Apoptosis in Rat Model with Chronic Nonbacterial Prostatitis.

Chronic prostatitis typically occurs in aging men, and its symptoms include frequent and painful urination. In recent study, several studies have shown that Korean red ginseng (KRG) can be used in the prevention and treatment of various diseases. The objective of this study is to investigate whether KRG can play a role in repressing the development of chronic nonbacterial prostatitis (CNP) in male Wistar rats. To induce CNP, rats were castrated and beta-estradiol (0.25 mg/kg) was subcutaneously (s.c.) injected daily. 7-week-old male Wistar rats were divided into 5 groups (the normal group, CNP group, positive group, and KRG group (0.25g/kg) and another KRG (0.50g/kg) group. After 4 weeks, all rats were sacrificed and their prostate and serum were analyzed. Compared to the positive group, the KRG groups (0.25g/kg and 0.50g/kg) showed similar protective properties on CNP based on the histopathologic morphology of the prostate and the inflammation cytokines in the prostate tissue. Also, results of the immunohistochemistry staining showed that expression levels of vascular endothelial growth factor A (VEGFA), interleukin 6 (IL6), interleukin 1 beta (IL-1ß), tumor necrosis factor (TNF-alpha), and cytochrome c oxidase subunit II (COX2) were also decreased in KRG group (0.25g/kg) and KRG group (0.50g/kg). These results suggested that KRG inhibited the development of CNP and might a useful herbal treatment or functional food for CNP.

Association Between Secretoglobin Family 3A Member 2 (SCGB3A2) Gene Polymorphisms and Asthma in a Korean Population.

BACKGROUND Secretoglobin family 3A member 2 (SCGB3A2) plays an important role in secreting lung surfactant protein, which is a downstream target of thyroid transcription factor. MATERIAL AND METHODS We investigated whether single-nucleotide polymorphisms (SNPs) of SCGB3A2 gene contribute to susceptibility to asthma. To explore this possible association, 2 promoter SNPs (rs6882292, 659 G/A and rs1368408, -112 G/A) and missense SNP (rs151333009, stop codon) were tested in SCGB3A2 gene in 101 asthma patients and 377 healthy control subjects. SNPStats was used to obtain odds ratio (OR), 95% confidence intervals (CI), and P value adjusted for age and sex as covariables. Logistic regression method in each model (dominant, recessive, and log-additive) was applied to analyze genetic data. RESULTS rs151333009 SNP showed a monomorphic genotype. Two promoter SNPs (rs6882292, -659 G/A and rs1368408, -112 G/A) showed significant association with asthma (rs6882292, OR=2.66, 95% CI=1.42-5.01, p=0.0033 in dominant model, OR=2.45, 95% CI=1.33-4.54, p=0.0055 in log-additive model; rs1368408, OR=1.59, 95% CI=1.02-2.49, p=0.041 in dominant model, OR=3.02, 95% CI=1.15-7.90, p=0.03 in recessive model, OR=1.63, 95% CI=1.63, 95% CI=1.12-2.37, p=0.012 in log-additive model). CONCLUSIONS These results suggest that the promoter SNPs (rs6882292 and rs1368408) of SCGB3A2 gene may contribute to susceptibility to asthma in a Korean population.

Inhibitory effect of curcumin on testosterone induced benign prostatic hyperplasia rat model.

BACKGROUND: Benign prostatic hyperplasia (BPH) is one of the common male diseases, which is provoked by dihydrotestosterone (DHT) and androgen signals. Several studies showed that curcumin has various effects of prevention and treatment to diseases. We investigated whether curcumin may repress the development of BPH in male Wistar rats. METHODS: Seven weeks male Wistar rats were and divided into 4 groups (normal group, BPH group, finasteride group, curcumin group; n = 8 for each group). In order to induce BPH in rats, rats were castrated and testosterone was injected subcutaneously everyday (s.c., 20 mg/kg). Rats in the curcumin group were treated 50 mg/kg, administered orally for 4 weeks. After 4 weeks, all rats were sacrificed and their prostate and serum were analyzed. RESULTS: Compared to the finasteride group as positive group, the curcumin group showed similarly protective effect on BPH in histopathologic morphology, prostate volume. Results of immunohistochemistry and western-blot showed decreased expressions of VEGF, TGF-ß1, and IGF1 were also decreased in the curcumin group. CONCLUSIONS: These results suggested that curcumin inhibited the development of BPH and might a useful herbal treatment or functional food for BPH.

An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length.

Efficient search algorithms for finding genomic-range overlaps are essential for various bioinformatics applications. A majority of fast algorithms for searching the overlaps between a query range (e.g., a genomic variant) and a set of N reference ranges (e.g., exons) has time complexity of O(k + logN), where kdenotes a term related to the length and location of the reference ranges. Here, we present a simple but efficient algorithm that reduces k, based on the maximum reference range length. Specifically, for a given query range and the maximum reference range length, the proposed method divides the reference range set into three subsets: always, potentially, and never overlapping. Therefore, search effort can be reduced by excluding never overlapping subset. We demonstrate that the running time of the proposed algorithm is proportional to potentially overlapping subset size, that is proportional to the maximum reference range length if all the other conditions are the same. Moreover, an implementation of our algorithm was 13.8 to 30.0 percent faster than one of the fastest range search methods available when tested on various genomic-range data sets. The proposed algorithm has been incorporated into a disease-linked variant prioritization pipeline for WGS (http://gnome.tchlab.org) and its implementation is available at http://ml.ssu.ac.kr/gSearch.

Estimating the composition of species in metagenomes by clustering of next-generation read sequences.

Faster and cheaper sequencing technologies together with the ability to sequence uncultured microbes collected from any environment present us an opportunity to distill meaningful information from the millions of new genomic sequences from environmental samples, called metagenome. Contrary to conventional cultured microbes, however, the metagenomic data is extremely heterogeneous and noisy. Therefore the separation of the sets of sequenced genomic fragments that belong to different microbes is essential for successful assembly of microbial genomes. In this paper, we present a novel clustering method for a given metagenomic dataset. The metagenomic dataset has some distinguished features because (i) it is possible that similar sequence patterns may exist in different species and (ii) each species has different number of individuals in the given metagenomic dataset. Our method overcomes these obstacles by using the Gaussian mixture model and analysis of mixture profiles, and taking advantage of genomic signatures extracted from the metagenomic dataset. Unlike conventional clustering methods where clusters are discovered through global similarities of data instances, our method builds clusters by combining the data instances sharing local similarities captured by mixture analysis. By considering shared mixture components, our method is able to create clusters of genomic sequences although they are globally distinct each other. We applied our method to an artificial metagenomic dataset comprised of simulated 47 million reads from 25 real microbial genomes, and analyzed the resulting clusters in terms of the number of clusters, the number of participating species and dominant species in each cluster. Even though our approach cannot address all challenges in the field of metagenome sequence clustering, we believe that out method can contribute to take a step forward to achieve the goals.

Association between TLR1 polymorphisms and alopecia areata.

Toll-like receptors (TLRs) may contribute to the process of autoimmune attacks on hair follicles. To investigate whether the TLR1 gene polymorphisms are associated with the development and clinical features of alopecia areata (AA), a case-control comparison of two single nucleotide polymorphisms (SNPs) (rs4833095, Asn248Ser and rs5743557, -414C > T) of TLR1 were studied in 239 AA patients and 248 controls. Using multiple logistic regression model, odds ratios, 95% confidence intervals and corresponding p values were estimated. Clinical features were analyzed based on the age of onset, family history, type of AA, nail involvement and body hair involvement. The missense SNP rs4833095 was significantly associated with the development of AA (codominant2, p = 0.002; recessive, p = 0.001; log-additive, p = 0.0071; and allele frequency, p = 0.0066). The promoter SNP rs5743557 was weakly associated with the development of AA (codominant2, p = 0.019; recessive, p = 0.032; log-additive, p = 0.020; and allele frequency, p = 0.03). In the clinical features, rs4833095 was only weakly associated with age of onset between 15 and 50 years (codominant2, p = 0.043 and recessive, p = 0.022). The results suggest that rs4833095 of TLR1 may be associated with the susceptibility for AA in the Korean population.

Association studies of cytochrome P450, family 2, subfamily E, polypeptide 1 (CYP2E1) gene polymorphisms with acute rejection in kidney transplantation recipients.

Recent studies have shown that single-nucleotide polymorphisms (SNPs) are associated with allograft rejection in kidney transplantation recipients. We evaluated the possible association between SNPs of the cytochrome P450, family 2, subfamily E, polypeptide 1 (CYP2E1) gene, and acute rejection (AR) among renal transplant patients in a Korean population. We conducted a case-control association study in 63 AR and 284 non-AR kidney transplant recipients. The SNPs of CYP2E1 were genotyped by direct sequencing. Recipient sex (p = 0.023) and the use of tacrolimus (p = 0.017) were significantly different between the two groups. The use of mycophenolate mofetil (MMF) and antibody induction therapy was significantly lower in the AR group. Multiple logistic regression models (codominant, dominant, recessive, and log-additive models) adjusted by sex and type of immunosuppressive regimens were applied to determine the odds ratios (ORs), 95% confidence intervals (CIs), and p-values. The rs2515641 of CYP2E1 showed significant differences between the AR patient group and non-AR group (p = 0.003, OR = 2.55, 95% CI = 1.37-4.75 in the codominant 1 model; p = 0.002, OR = 2.61, 95% CI = 1.43-4.77 in the dominant model; p = 0.0035, OR = 2.13, 95% CI = 1.29-3.50 in the log-additive model). The allele of the rs2515641 SNP also showed a significant association (p = 0.004, OR = 1.99, 95% CI = 1.24-3.21). This study suggests that the CYP2E1 polymorphism may be related to the development of AR in Korean kidney transplantation recipients.

Association study between monoamine oxidase A (MAOA) gene polymorphisms and schizophrenia: lack of association with schizophrenia and possible association with affective disturbances of schizophrenia.

Monoamine oxidase A (MAOA) catalyzes monoamine neurotransmitters including dopamine, 5-hydroxytryptamine (5-HT, serotonin), and norepinephrine. MAOA also plays a key role in emotional regulation. The aim of this study was to investigate the associations between the exonic single nucleotide polymorphisms (SNPs) of the MAOA gene located on the X chromosome and schizophrenia. We also analyzed the relationships between these SNPs and the common clinical symptoms of schizophrenia such as persecutory delusion, auditory hallucinations, affective disturbances, and poor concentration. Two hundred seventy five Korean schizophrenia patients and 289 control subjects were recruited. Three SNPs [rs6323 (Arg294Arg), rs1137070 (Asp470Asp), and rs3027407 (3'-untranslated region)] of the MAOA gene were selected and genotyped by direct sequencing. The common clinical symptoms of schizophrenia according to the Operation Criteria Checklist were analyzed. Three examined SNPs showed no associations with male and female schizophrenia, respectively (p>0.05). In the analysis of the common clinical symptoms of schizophrenia patients, three examined SNPs were associated with affective disturbances, especially restricted affect and blunted affect in male schizophrenia, respectively (restricted affect, p=0.002, OR=2.71, 95% CI 1.45-5.00; blunted affect, p=0.009, OR 2.25, 95% CI 1.22-4.12). The SNPs were not associated with other clinical symptoms of schizophrenia (persecutory delusion, auditory hallucinations, and poor concentration). These results suggest that exonic SNPs (rs6323, rs1137070, and rs3027407) of the MAOA gene may be contributed to affective disturbances of Korean males schizophrenia, especially restricted affect and blunted affect.

Association between interleukin 18 polymorphisms and alopecia areata in Koreans.

Interleukin 18 (interferon gamma-inducing factor) (IL18) is an important proinflammatory cytokine that belongs to the IL1 family. This study investigated whether IL18 single-nucleotide polymorphisms (SNPs) are associated with the susceptibility to alopecia areata (AA) in a Korean population. Two hundred thirty-three AA patients and 243 healthy control subjects were recruited. One promoter SNP (rs187238, -137G/C) and exonic SNP (rs549908, Ser35Ser) in IL18 were genotyped using direct sequencing. SNPStats, SPSS 18.0, and Haploview version 4.2 programs were used to evaluate genetic data. Multiple logistic regression models were used to determine odds ratios, 95% confidence intervals, and P values. Tested 2 SNPs (rs187238 and rs549908) were associated with the development of AA (rs187238, P=0.002 in a codominant model 1, P=0.0048 in a dominant model, P=0.02 in a log-additive model, P=0.023 in allele distribution; rs549908, P=0.003 in a codominant model 1, P=0.0052 in a dominant model, P=0.016 in a log-additive model, P=0.015 in allele distribution). Our data suggest that the IL18 may be a risk factor for AA susceptibility.

Association of BID SNPs (rs8190315 and rs2072392) and clinical features of benign prostate hyperplasia in Korean population.

Exercise has beneficial effect on cancer apoptosis and benign prostatic hyperplasia (BPH). The BH3 interacting domain death agonist (BID) gene expression is associated with apoptosis or cell proliferation. In this study, we investigated the association between BID single nucleotide polymorphisms (SNPs) and the development, prostate volume, and international prostate symptom score (IPSS) of BPH. In 222 BPH males and 214 controls, two SNPs in BID [rs8190315 (Ser56Gly), and rs2072392 (Asp106Asp)] were genotyped and analyzed using multiple logistic regression models. In the result, the genotype and allele frequencies of rs8190315 and rs2072392 were not associated with BPH development or IPSS, however, the allele frequencies [odd ratio (OR)= 1.90, 95% confidence interval (CI)= 1.07-3.41, P= 0.03] and genotype frequencies (in dominant model, OR= 1.94, 95% CI= 1.01-3.74, P= 0.42) of rs8190315, and the genotype frequencies of rs2072392 (in dominant model, OR= 1.94, 95% CI= 1.01-3.74, P= 0.42) were associated with increased prostate volume. We propose that rs8190315 and rs2072392 of BID may contribute to the disease severity of BPH.

Association of HSPA1B SNP rs6457452 with Alopecia Areata in the Korean population.

The heat shock 70 kDa protein 1B (HSPA1B), which has been well-studied among the famous heat shock proteins HSPA1A/B/L, is related to autoimmune diseases, including Alopecia Areata (AA). In this study, the association of a 5'-untranslated region (5'UTR) SNP rs6457452 and a promoter SNP rs2763979 (-1140C > T) of HSPA1B with AA was investigated in 236 controls and 228 AA patients. Statistical analyses using the multiple logistic models were done, according to the onset and the clinical features of AA, including the age of onset, family history, type of AA lesion, nail involvement and body hair involvement. The results showed that rs6457452 was associated with the onset of AA (p < 0.002). In the analysis of clinical features of AA, rs6457452 was weakly related to the age of onset (p ≤ 0.04) and that rs2763979 was only weakly related to the type of AA lesion (p = 0.041). In conclusion, we suggest that the 5'UTR SNP rs6457452 of HSPA1B may be associated with the onset of AA and the T allele of rs6457452 may confer the reduced susceptibility to AA in the Korean population.

The effects of platelet-rich clot releasate on the expression of MMP-1 and type I collagen in human adult dermal fibroblasts: PRP is a stronger MMP-1 stimulator.

Platelet-rich plasma is widely used in acute and chronic ulcers due to its capacity to enhance the wound healing process. Fibroblasts are believed to be the most important cells in the production and remodeling of the extracellular matrix (ECM). Matrix metalloproteinase (MMP)-1 is the proteolytic enzyme of collagen I, and has a key role in collagen remodeling during wound healing. Whether or not platelet-rich clot releasate (PRCR) is able to effectively modulate the ECM, and the effect of PRCR on the expression of type I collagen and MMP-1 in human dermal fibroblasts was evaluated. Specifically, human adult dermal fibroblasts were incubated in PRCR-containing solutions for 24 and 48 h, after which the levels of collagen and MMP-1 were quantified by reverse transcription PCR at the transcriptional level, and ELISA and immunoblot analyses at the post-transcriptional level. PRCR markedly up-regulated the expression of MMP-1 and type I collagen in fibroblasts incubated in 20 % PRCR solutions for 48 h. These findings suggest that increased MMP-1 expression after PRCR treatment enable remodeling the ECM.

Missense polymorphisms in XIAP-associated factor-1 (XAF1) and risk of papillary thyroid cancer: correlation with clinicopathological features.

X-Linked inhibitor of apoptosis (XIAP)-associated factor-1 (XAF1) antagonizes XIAP-mediated caspase inhibition. XAF1 also serves as a tumor-suppressor gene, and loss of XAF1 expression correlates with tumor progression. This study investigated whether XAF1 missense single-nucleotide polymorphisms (SNPs) are associated with the development of papillary thyroid cancer (PTC) and their clinicopathological features in a Korean population. Eighty-nine cases of PTC and 276 controls were enrolled. Two missense SNPs [rs34195599 (Glu85Gly) and rs2271232 (Arg132His)] in XAF1 were genotyped using direct sequencing. The SNPStats, SNPAnalyzer, Helixtree, and Haploview version 4.2 programs were used to evaluate genetic data. Multiple logistic regression models were used to determine odds ratios (ORs), 95% confidence intervals (CIs), and p-values. Missense SNP rs34195599 was weakly-associated with the development of PTC (p=0.046 in genotypic distributions; p=0.048 in allelic distributions). For the clinicopathological features, rs34195599 was strongly related to multifocality [unifocality (A/G, 1.7%) vs. multifocality (A/G, 16.7%), OR=11.44, 95% CI=1.27-103.26, p=0.015 in genotypic distributions] [unifocality (G, 0.8%) vs. multifocality (G, 8.3%), OR=10.64, 95% CI=1.21-93.23, p=0.017 in allelic distributions] and location [one lobe (A/G, 1.6%) vs. both lobes (A/G, 19.2%), OR=15.63, 95% CI=1.62-150.46, p=0.008 in genotypic distributions] [one lobe (G, 0.8%) vs. both lobes (G, 9.6%), OR=13.30, 95% CI=1.51-116.82, p=0.009 in allelic distributions]. Our data suggest that the G allele of rs34195599 of XAF1 may be a risk factor for the clinicopathological features of PTC, especially for multifocality and location (both lobes).

Association of a Missense ALDH2 Single Nucleotide Polymorphism (Glu504Lys) With Benign Prostate Hyperplasia in a Korean Population.

PURPOSE: Aldehyde dehydrogenase 2 (ALDH2) is a well-known gene involved in alcohol and aldehyde metabolism. Moreover, recent studies have reported associations between ALDH2 and age-related disorders. Benign prostate hyperplasia (BPH) is an age-related disorder and genetic factors may contribute to its onset. In this study, we investigated the association of a well-studied ALDH2 single nucleotide polymorphism (SNP), rs671, with the onset and clinical features of BPH. METHODS: A total of 222 BPH patients and 214 control subjects were genotyped. The clinical features of the BPH patients (prostate volume, prostate-specific antigen level, and International Prostatic Symptom Score) were analyzed. RESULTS: The results show that rs671 was only associated with the volume of BPH in genotype and allele frequencies (P<0.05). CONCLUSION: We propose that rs671 is an Asian-specific SNP in ALDH2 that may affect the disease progression of BPH in the Korean population.

Association between regulating synaptic membrane exocytosis 2 gene polymorphisms and degenerative lumbar scoliosis.

Degenerative lumbar scoliosis (DLS) is a spinal deformity that develops after skeletal maturity and progresses with age. In contrast to adolescent idiopathic scoliosis, the genetic association of DLS has not yet been elucidated. The purpose of this study was to investigate the association between regulating synaptic membrane exocytosis 2 (RIMS2, OBOE) gene polymorphisms and DLS. Two coding single-nucleotide polymorphisms [rs2028945 (Gln1200Gln) and rs10461 (Ala1327Ala)] of RIMS2 were selected and genotyped by direct sequencing. As a result, the rs10461 was associated with DLS in allele frequencies (P=0.008) and genotype distributions (P=0.006 in the codominant model, 0.018 in the dominant model and 0.029 in the recessive model). In the analysis of haplotypes, two haplotypes exhibited significant differences between the control and DLS groups (CC haplotype, P=0.009 in the codominant model, 0.038 in the dominant model and 0.030 in the recessive model; CT haplotype, P=0.041 in the codominant model and 0.021 in the dominant model). These findings suggest that RIMS2 may be associated with the development of DLS.

Association of annexin A5 polymorphisms with obesity.

Annexin A5 (ANXA5), which is known as a protein with anticoagulative function, may play a role in triglyceride biosynthesis. Triglycerides are involved in lipid and energy metabolism, which are important in the elucidation of obesity. To investigate the association between single-nucleotide polymorphisms (SNPs) of ANXA5 and obesity in a Korean population, 372 participants (213 overweight/obese individuals and 159 control subjects) were enrolled from the Kyung Hee University Medical Center and Keimyung University Dongsan Medical Center. The genotypes of five SNPs (rs12510548, rs4240260, rs3756281, rs13136094 and rs6534313) were evaluated in ANXA5 using the multiple logistic regression analysis with the codominant 1, codominant 2, dominant, recessive and log-additive models. The genotype and allele frequencies of the five investigated SNPs exhibited significant differences between the control and the overweight/obese groups: rs12510548 (P=0.004 in the codominant 2 model, P=0.0019 in the recessive model, P=0.027 in the log-additive model and P=0.026 in allele frequencies); rs4240260 (P=0.002 and Fisher's exact P=0.0006 in the codominant 2 model, P=0.0007 and Fisher's exact P=0.0007 in the recessive model, P=0.020 and Fisher's exact P=0.0019 in the log-additive model and P=0.020 in allele frequencies); rs3756281 (P=0.016 in the codominant 2 model and P=0.0094 in the recessive model); rs13136094 (P=0.0030 and Fisher's exact P=0.0011 in the codominant 2 model, P=0.0012 and Fisher's exact P=0.0013 in the recessive model, P=0.034 and Fisher's exact P=0.0035 in the log-additive model and P=0.024 in allele frequencies); and rs6534313 (P=0.0010 and Fisher's exact P=0.0003 in the codominant 2 model, P=0.0003 and Fisher's exact P=0.0003 in the recessive model, P=0.0075 and Fisher's exact P=0.0010 in the log-additive model and P=0.005 in allele frequencies). Two haplotypes were weakly associated with obesity (GGATG, P=0.037 and CAGCC, P=0.020). Results of the present study suggested that ANXA5 may be associated with the development of obesity in a Korean population.