• 제목/요약/키워드: metabolic networks

Search Result 54, Processing Time 0.02 seconds

Profiling of glucose-induced transcription in Sulfolobus acidocaldarius DSM 639

  • Park, Jungwook;Lee, Areum;Lee, Hyun-Hee;Park, Inmyoung;Seo, Young-Su;Cha, Jaeho
    • Genes and Genomics
    • /
    • v.40 no.11
    • /
    • pp.1157-1167
    • /
    • 2018
  • Sulfolobus species can grow on a variety of organic compounds as carbon and energy sources. These species degrade glucose to pyruvate by the modified branched Entner-Doudoroff pathway. We attempted to determine the differentially expressed genes (DEGs) under sugar-limited and sugar-rich conditions. RNA sequencing (RNA-seq) was used to quantify the expression of the genes and identify those DEGs between the S. acidocaldarius cells grown under sugar-rich (YT with glucose) and sugar-limited (YT only) conditions. The functions and pathways of the DEGs were examined using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Quantitative real-time PCR (qRT-PCR) was performed to validate the DEGs. Transcriptome analysis of the DSM 639 strain grown on sugar-limited and sugar-rich media revealed that 853 genes were differentially expressed, among which 481 were upregulated and 372 were downregulated under the glucose-supplemented condition. In particular, 70 genes showed significant changes in expression levels of ${\geq}$ twofold. GO and KEGG enrichment analyses revealed that the genes encoding components of central carbon metabolism, the respiratory chain, and protein and amino acid biosynthetic machinery were upregulated under the glucose condition. RNA-seq and qRT-PCR analyses indicated that the sulfur assimilation genes (Saci_2197-2204) including phosphoadenosine phosphosulfate reductase and sulfite reductase were significantly upregulated in the presence of glucose. The present study revealed metabolic networks in S. acidocaldarius that are induced in a glucose-dependent manner, improving our understanding of biomass production under sugar-rich conditions.

C4orf47 is a Novel Prognostic Biomarker and Correlates with Infiltrating Immune Cells in Hepatocellular Carcinoma

  • Hye-Ran Kim;Choong Won Seo;Sang Jun Han;Jongwan Kim
    • Biomedical Science Letters
    • /
    • v.29 no.1
    • /
    • pp.11-25
    • /
    • 2023
  • In hepatocellular carcinoma (HCC), chromosome 4 open-reading frame 47 (C4orf47) has not been so far investigated for its prognostic value or association with infiltrating immune cells. We performed bioinformatics analysis on HCC data and analyzed the data using online databases such as TIMER, UALCAN, Kaplan-Meier plotter, LinkedOmics, and GEPIA2. We found that C4orf47 expression in HCC was higher compared to normal tissues. High C4orf47 expression was associated with a worse prognosis in HCC. The correlation between C4orf47 and infiltrating immune cells is positively associated with CD4+T cells, B cells, neutrophils, macrophages, and dendritic cells in HCC. Moreover, high C4orf47 expression was correlated with a poor prognosis of infiltrating immune cells. Analysis of C4orf47 gene co-expression networks revealed that 12501 genes were positively correlated with C4orf47, whereas 7200 genes were negatively correlated. The positively related genes of C4orf47 are associated with a high hazard ratio in different types of cancer, including HCC. Regarding the biological functions of C4orf47 gene, it mainly regulates RNA metabolic process, DNA replication, and cell cycle. The C4orf47 gene may play a prognostic role by regulating the global transcriptome process in HCC. Our findings demonstrate that high C4orf47 expression correlates with poor prognosis and tumor-infiltrating immune cells in HCC. We suggest that C4orf47 is a novel prognostic biomarker and potential immune therapeutic target for HCC.

Systems Pharmacological Analysis of Dichroae Radix in Anti-Tumor Metastasis Activity (시스템 약리학적 분석에 의한 상산의 암전이 억제 효과)

  • Jee Ye Lee;Ah Yeon Shin;Hak Koon Kim;Won Gun An
    • Herbal Formula Science
    • /
    • v.31 no.4
    • /
    • pp.295-313
    • /
    • 2023
  • Objectives : While treatments for cancer are advancing, the development of effective treatments for cancer metastasis, the main cause of cancer patient death, remains insufficient. Recent studies on Dichroae Radix have revealed that its active ingredients have the potential to inhibit cancer metastasis. This study aimed to investigate the cancer metastasis inhibitory effect of Dichroae Radix using network pharmacological analysis. Methods : The active compounds of Dichroae Radix have been identified using Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The UniProt database was used to collect each of information of all target proteins associated with the active compounds. To find the bio-metabolic processes associated with each target, the DAVID6.8 Gene Functional classifier tool was used. Compound-Target and Target-Pathway networks were analyzed via Cytoscape 3.40. Results : In total, 25 active compounds and their 62 non-redundant targets were selected through the TCMSP database and analysis platform. The target genes underwent gene ontology and pathway enrichment analysis. The gene list applied to the gene ontology analysis revealed associations with various biological processes, including signal transduction, chemical synaptic transmission, G-protein-coupled receptor signaling pathways, response to xenobiotic stimulus, and response to drugs, among others. A total of eleven genes, including HSP90AB1, CALM1, F2, AR, PAKACA, PTGS2, NOS2, RXRA, ESR1, ESR2, and NCOA1, were found to be associated with biological pathways related to cancer metastasis. Furthermore, nineteen of the active compounds from Dichroae Radix were confirmed to interact with these genes. Conclusions : The results provide valuable insights into the mechanism of action and molecular targets of Dichroae Radix. Notably, Berberine, the main active ingredient of Dichroae Radix, plays a significant role in degrading AR proteins in advanced prostate cancer. Further studies and validations can provide crucial data to advance cancer metastasis prevention and treatment strategies.

Development and application of prediction model of hyperlipidemia using SVM and meta-learning algorithm (SVM과 meta-learning algorithm을 이용한 고지혈증 유병 예측모형 개발과 활용)

  • Lee, Seulki;Shin, Taeksoo
    • Journal of Intelligence and Information Systems
    • /
    • v.24 no.2
    • /
    • pp.111-124
    • /
    • 2018
  • This study aims to develop a classification model for predicting the occurrence of hyperlipidemia, one of the chronic diseases. Prior studies applying data mining techniques for predicting disease can be classified into a model design study for predicting cardiovascular disease and a study comparing disease prediction research results. In the case of foreign literatures, studies predicting cardiovascular disease were predominant in predicting disease using data mining techniques. Although domestic studies were not much different from those of foreign countries, studies focusing on hypertension and diabetes were mainly conducted. Since hypertension and diabetes as well as chronic diseases, hyperlipidemia, are also of high importance, this study selected hyperlipidemia as the disease to be analyzed. We also developed a model for predicting hyperlipidemia using SVM and meta learning algorithms, which are already known to have excellent predictive power. In order to achieve the purpose of this study, we used data set from Korea Health Panel 2012. The Korean Health Panel produces basic data on the level of health expenditure, health level and health behavior, and has conducted an annual survey since 2008. In this study, 1,088 patients with hyperlipidemia were randomly selected from the hospitalized, outpatient, emergency, and chronic disease data of the Korean Health Panel in 2012, and 1,088 nonpatients were also randomly extracted. A total of 2,176 people were selected for the study. Three methods were used to select input variables for predicting hyperlipidemia. First, stepwise method was performed using logistic regression. Among the 17 variables, the categorical variables(except for length of smoking) are expressed as dummy variables, which are assumed to be separate variables on the basis of the reference group, and these variables were analyzed. Six variables (age, BMI, education level, marital status, smoking status, gender) excluding income level and smoking period were selected based on significance level 0.1. Second, C4.5 as a decision tree algorithm is used. The significant input variables were age, smoking status, and education level. Finally, C4.5 as a decision tree algorithm is used. In SVM, the input variables selected by genetic algorithms consisted of 6 variables such as age, marital status, education level, economic activity, smoking period, and physical activity status, and the input variables selected by genetic algorithms in artificial neural network consist of 3 variables such as age, marital status, and education level. Based on the selected parameters, we compared SVM, meta learning algorithm and other prediction models for hyperlipidemia patients, and compared the classification performances using TP rate and precision. The main results of the analysis are as follows. First, the accuracy of the SVM was 88.4% and the accuracy of the artificial neural network was 86.7%. Second, the accuracy of classification models using the selected input variables through stepwise method was slightly higher than that of classification models using the whole variables. Third, the precision of artificial neural network was higher than that of SVM when only three variables as input variables were selected by decision trees. As a result of classification models based on the input variables selected through the genetic algorithm, classification accuracy of SVM was 88.5% and that of artificial neural network was 87.9%. Finally, this study indicated that stacking as the meta learning algorithm proposed in this study, has the best performance when it uses the predicted outputs of SVM and MLP as input variables of SVM, which is a meta classifier. The purpose of this study was to predict hyperlipidemia, one of the representative chronic diseases. To do this, we used SVM and meta-learning algorithms, which is known to have high accuracy. As a result, the accuracy of classification of hyperlipidemia in the stacking as a meta learner was higher than other meta-learning algorithms. However, the predictive performance of the meta-learning algorithm proposed in this study is the same as that of SVM with the best performance (88.6%) among the single models. The limitations of this study are as follows. First, various variable selection methods were tried, but most variables used in the study were categorical dummy variables. In the case with a large number of categorical variables, the results may be different if continuous variables are used because the model can be better suited to categorical variables such as decision trees than general models such as neural networks. Despite these limitations, this study has significance in predicting hyperlipidemia with hybrid models such as met learning algorithms which have not been studied previously. It can be said that the result of improving the model accuracy by applying various variable selection techniques is meaningful. In addition, it is expected that our proposed model will be effective for the prevention and management of hyperlipidemia.