• BMB Reports
• /
• 제45권2호
• /
• pp.120-125
• /
• 2012

We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.

• Asian-Australasian Journal of Animal Sciences
• /
• 제30권2호
• /
• pp.160-166
• /
• 2017

Objective: This study identifies single-nucleotide polymorphisms (SNP) or gene combinations that affect the flavor and quality of Korean cattle (Hanwoo) by using the SNP Harvester method. Methods: Four economic traits (oleic acid [C18:1], saturated fatty acids), monounsaturated fatty acids, and marbling score) were adjusted for environmental factors in order to focus solely on genetic effects. The SNP Harvester method was used to investigate gene combinations (two-way gene interactions) associated with these economic traits. Further, a multifactor dimensionality reduction method was used to identify superior genotypes in gene combinations. Results: Table 3 to 4 show the analysis results for differences between superior genotypes and others for selected major gene combinations using the multifactor dimensionality reduction method. Environmental factors were adjusted for in order to evaluate only the genetic effect. Table 5 shows the adjustment effect by comparing the accuracy before and after correction in two-way gene interactions. Conclusion: The g.3977-325 T>C and (g.2988 A>G, g.3977-325 T>C) combinations of fatty acid-binding protein4 were the superior gene, and the superior genotype combinations across all economic traits were the CC genotype at g.3977-325 T>C and the AACC, GACC, GGCC genotypes of (g.2988 A>G, g.3977-325 T>C).

• 대한의생명과학회지
• /
• 제24권4호
• /
• pp.334-340
• /
• 2018

The cytoplasmic elicitor, nucleotide-binding domain and leucine-rich repeat containing domain receptors (NLRs) is well established molecules in its role in inflammatory response. Among 22 NLR receptors, NOD2 is one of the intensively studied genes of elucidating for the inflammatory bowel disease and Crohn's disease as well. Recent research have accumulated that common genetic mutations in Parkinson's disease (PD) are increasingly related to the susceptibility to Crohn's disease. In this study, with the Korean Genome and Epidemiology Study, we aimed to perform the association between NOD2 polymorphisms and blood cell counts [WBC (white blood cell) count, RBC (red blood cell) count, platelet count], which linked supposedly to cytoplasmic inflammatory responses with clinical specialty. Linear regression analyses were performed, controlling for residential area, sex, and age as covariates. As a results, 12 SNPs from NOD2 gene were significantly associated with WBC counts (Bonferroni correction P-value criteria < 0.05/23=0.00218). In this study, we could ensure an association with NOD2 gene and WBC counts. This is the first report to have relationship between SNPs of NOD2 gene and WBC counts.

• 생물정신의학
• /
• 제29권2호
• /
• pp.33-39
• /
• 2022

Objectives The early growth response 3 (EGR3) gene located in chromosome 8p21.3 is one of the susceptibility loci in many psychiatric disorders. EGR3 gene plays critical roles in signal transduction in the brain, which is involved in neuronal plasticity, neuronal development, learning, memory, and circadian rhythms. Recent studies have suggested EGR3 as a potential susceptibility gene for bipolar disorder (BPD). However, this requires further replication with an independent sample set. Methods To investigate the genetic role of EGR3 in Korean patients, we genotyped six single-nucleotide polymorphisms (SNPs) in the chromosome region of EGR3 in 1076 Korean BPD patients and 773 healthy control subjects. Results Among the six examined SNPs of EGR3 (rs17088531, rs1996147, rs3750192, rs35201266, rs7009708, rs1008949), SNP rs35201266, rs7009708, rs1008949 showed a significant association with BPD (p = 0.0041 for rs35201266 and BPD2, p = 0.0074 for rs1008949 and BPD, p = 0.0052 for rs1008949 and BPD1), which withstand multiple testing correction. In addition, the 'G-C-C-C' and 'G-C-G-C' haplotypes of EGR3 were overrepresented in the patients with BPD (p = 0.0055, < 0.0001, respectively) and the 'G-T-G-C' haplotype of EGR3 was underrepresented in patients with BPD (p = 0.0040). Conclusions In summary, our study supports the association of EGR3 with BPD in Korean population sample, and EGR3 could be suggested as a compelling susceptibility gene in BPD.

• Journal of Korean Dental Science
• /
• 제6권2호
• /
• pp.41-49
• /
• 2013

Purpose: This study sought to compare the elemental constitution, morphological characteristics, particle size distribution, biocompatibility, and mineralization potential of Ortho MTA (OMTA) and ProRoot MTA (PMTA). Materials and Methods: OMTA and PMTA were compared using energy-dispersive spectrometry, particle size analysis, and scanning electron microscopy. The biocompatibility and mineralization-related gene expression (osteonectin and osteopontin) of both MTAs were also compared using methylthiazol tetrazolium assay and reverse transcription-polymerization chain reaction analysis, respectively. The results were analyzed by Kruskal-Wallis test with Bonferroni correction. P-value of <0.05 was considered significant. Result: The morphology of OMTA powders was similar to that of PMTA. The constituent elements of both MTAs were calcium, silicon, and aluminum. The mean particle sizes of OMTA and PMTA were 4.60 and 3.34 mm, respectively. Both MTAs had equally favorable in vitro biocompatibility and affected the messenger RNA expression of osteonectin and osteopontin. Conclusion: Within the limitations of this study, OMTA could be a promising biomaterial in clinical endodontics.

• Genomics & Informatics
• /
• 제1권2호
• /
• pp.94-100
• /
• 2003

Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

• Animal Bioscience
• /
• 제37권3호
• /
• pp.451-460
• /
• 2024

Objective: The objective is to identify genomic regions and candidate genes associated with age to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) in Yorkshire pig. Methods: This study used a total of 104,380 records and 11,854 single nucleotide polymorphism (SNP) data obtained from Illumina porcine 60K chip. The estimated genomic breeding values (GEBVs) and SNP effects were estimated by single-step genomic best linear unbiased prediction (ssGBLUP). Results: The heritabilities of AGE, ADG, BF, and EMA were 0.50, 0.49, 0.49, and 0.23, respectively. We identified significant SNP markers surpassing the Bonferroni correction threshold (1.68×10^-6), with a total of 9 markers associated with both AGE and ADG, and 4 markers associated with BF and EMA. Genome-wide association study (GWAS) analyses revealed notable chromosomal regions linked to AGE and ADG on Sus scrofa chromosome (SSC) 1, 6, 8, and 16; BF on SSC 2, 5, and 8; and EMA on SSC 1. Additionally, we observed strong linkage disequilibrium on SSC 1. Finally, we performed enrichment analyses using gene ontology and Kyoto encyclopedia of genes and genomes (KEGG), which revealed significant enrichments in eight biological processes, one cellular component, one molecular function, and one KEGG pathway. Conclusion: The identified SNP markers for productive traits are expected to provide valuable information for genetic improvement as an understanding of their expression.

• Genomics & Informatics
• /
• 제5권1호
• /
• pp.10-18
• /
• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• 생물정신의학
• /
• 제11권2호
• /
• pp.136-145
• /
• 2004

Objectives:Genetic variations of the tryptophan hydroxylase(TPH) gene and the serotonin transporter linked polymorphic region(5-HTTLPR) polymorphism have been associated with its functional capacity. The authors investigated whether the allelic constitution of the TPH gene and 5-HTTLPR are associated in Korean panic patients. Methods:244 Korean patients with panic disorder and 227 normal healthy controls were tested for a genetic polymorphism of TPH A218C and 5-HTTLPR polymorphism. To assess the severity of panic disorder during the last one month, anticipatory anxiety, panic difficulty, panic distress, agoraphobic difficulty and agoraphobic distress were measured with visual analogue scale(VAS) score, STAI-S & T, BDI, SCL-90-R, ASI-R, CGI, PDSS, and HAMD. Results:There was no significant difference in genotype and allele frequencies of TPH A218C and 5-HTTLPR polymorphism between panic patients and controls. Although we observed some differences in genotype and allele frequencies of TPH A218C polymorphism among male subjects, these differences disappeared after Bonferroni correction. And there were no significant differences in clinical variables. Conclusion:Our results suggested that there are no association between the genetic polymorphism of TPH gene and 5-HTTLPR with panic disorder.

• Toxicological Research
• /
• 제26권1호
• /
• pp.21-28
• /
• 2010

As the frequency and the intensity of so called Asian dust (AD) events have increased, public concerns about the adverse health effects has spiked sharply over the last two decades. Despite the recent reports on the correlation between AD events and the risk for cardiovascular and respiratory disease, the nature of the toxicity and the degree of the risk are yet largely unknown. In the present study, we investigated the effects of the dichloromethane extract of AD (AD-X) and that of urban dust (NAD-X) collected during a non-AD period on gene expression in HL-60 cells using Illumina Sentrix HumanRef-8 Expression BeadChips. Global changes in gene expression were analyzed after 24 h of incubation with 50 or 100 ${\mu}g$/ml AD-X and NAD-X. By one-way analysis of variance (p < 0.05) and Benjamini-Hochberg multiple testing correction for false discovery rate of the results, 573 and 297 genes were identified as AD-X- and NAD-X-responsive, respectively. The genes were classified into three groups by Venn diagram analysis of their expression profile, i.e., 290 AD-X-specific, 14 NAD-X-specific, and 283 overlapping genes. Quantitative realtime PCR confirmed the changes in the expression levels of the selected genes. The expression patterns of five genes, namely SORL1, RABEPK, DDIT4, AZU1, and NUDT1 differed significantly between the two groups. Following rigorous validation process, these genes may provide information in developing biomarker for AD exposure.