RESUMO
Summary: Large-scale phosphoproteomics studies have improved our understanding of dynamic cellular signaling, but the downstream analysis of phosphoproteomics data is still a bottleneck. We develop DynaPho, a useful web-based tool providing comprehensive and in-depth analyses of time-course phosphoproteomics data, making analysis intuitive and accessible to non-bioinformatics experts. The tool currently implements five analytic modules, which reveal the transition of biological pathways, kinase activity, dynamics of interaction networks and the predicted kinase-substrate associations. These features can assist users in translating their larger-scale time-course phosphoproteomics data into valuable biological discoveries. Availability and implementation: DynaPho is freely available at http://dynapho.jhlab.tw/ . Contact: hsuancheng@ym.edu.tw or yukijuan@ntu.edu.tw . Supplementary information: Supplementary data are available at Bioinformatics online.
RESUMO
Long non-coding RNAs (lncRNAs) have been found to play important roles in various biological processes; however, many of their functions remain unclear. In this study, we present a novel approach to identify the lncRNA-associated protein-protein interaction (PPI) modules and ascertain their functions in human lung squamous cell carcinoma. We collected lncRNA and mRNA expression profiles of lung squamous cell carcinoma from The Cancer Genome Atlas. To identify the lncRNA-associated PPI modules, lncRNA-mRNA co-expression networks were first constructed based on the mutual ranks of expression correlations. Next, we examined whether the co-expressed mRNAs of a specific lncRNA were closely connected by PPIs. For this, a significantly connected mRNA set was considered to be the lncRNA-associated PPI module. Finally, the prospective functions of a lncRNA was inferred using Gene Ontology enrichment analysis on the associated module. We found that lncRNA-associated PPI modules were subtype-dependent and each subtype had unique molecular mechanisms. In addition, antisense lncRNAs and sense genes tended to be functionally associated. Our results might provide new directions for understanding lncRNA regulations in lung cancer. The analysis pipeline was implemented in a web tool, available at http://lncin.ym.edu.tw/.
Assuntos
Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/metabolismo , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Bases de Dados de Ácidos Nucleicos , Perfilação da Expressão Gênica , Transportador de Glucose Tipo 1/genética , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , Mapas de Interação de Proteínas , RNA Antissenso/genética , RNA Antissenso/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Neoplásico/genética , RNA Neoplásico/metabolismoRESUMO
Lignans, a class of dimeric phenylpropanoid derivative found in plants, such as whole grains and sesame and flax seeds, have anticancer activity and can act as phytoestrogens. The lignans secoisolariciresinol and matairesinol can be converted in the mammalian proximal colon into enterolactone and enterodiol, respectively, which reduce the risk of breast and colon cancer. To establish an efficient bioconversion system to generate matairesinol from pinoresinol, the genes encoding pinoresinol-lariciresinol reductase (PLR) and secoisolariciresinol dehydrogenase (SDH) were cloned from Podophyllum pleianthum Hance, an endangered herb in Taiwan, and the recombinant proteins, rPLR and rSDH, were expressed in Escherichia coli and purified. The two genes, termed plr-PpH and sdh-PpH, were also linked to form two bifunctional fusion genes, plr-sdh and sdh-plr, which were also expressed in E. coli and purified. Bioconversion in vitro at 22°C for 60 min showed that the conversion efficiency of fusion protein PLR-SDH was higher than that of the mixture of rPLR and rSDH. The percent conversion of (+)-pinoresinol to matairesinol was 49.8% using PLR-SDH and only 17.7% using a mixture of rPLR and rSDH. However, conversion of (+)-pinoresinol by fusion protein SDH-PLR stopped at the intermediate product, secoisolariciresinol. In vivo, (+)-pinoresinol was completely converted to matairesinol by living recombinant E. coli expressing PLR-SDH without addition of cofactors.
Assuntos
Escherichia coli/genética , Escherichia coli/metabolismo , Furanos/metabolismo , Lignanas/metabolismo , Biotransformação , Engenharia Metabólica , Dados de Sequência MolecularRESUMO
This study aims to examine how help-seeking behaviors of Chinese Americans are associated with the types of mental disorder, the tendency to somatize symptoms, social disruptiveness of symptoms, and comorbidity. Based on data from the Chinese American Psychiatric Epidemiological Study, we examined 246 Chinese Americans with a diagnosable major depressive disorder, anxiety disorder, or somatoform disorder, using hierarchical logistic regression analyses. Compared with respondents with somatoform disorder, those with anxiety or depressive disorder were 94% and 87% less likely to seek professional help. The tendency to somatize distress is positively related to soliciting help, especially medical help. Social disruptiveness had a very potent positive association with help seeking whereas comorbidity is nonsignificant when the symptom severity is controlled. The overall picture indicates that somatic expression of distress is a major impetus to help seeking, which happens to concur with the cultural conceptualization and subjective embodied experience of mental disorders among Chinese.
