NPBS database: a chemical data resource with relational data between natural products and biological sources

Xu, Tingjun; Chen, Wei-Ming; Zhou, Junhong; Dai, Jixun; Li, Yingyong; Zhao, Yingli

doi:10.1093/database/baaa102

Cited by 19 publications

(17 citation statements)

References 24 publications

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“…Ferroptosis related genes were obtained from three databases. 177 ferroptosis regulators (including 108 drivers, 69 suppressors) and 111 ferroptosis markers were found from FerrDb database 4 [ 36 ]. 25 ferroptosis-related genes were obtained in the ferroptosis pathway (map04216) from the KEGG PATHWAY Database.…”

Section: Methodsmentioning

confidence: 99%

Characterization of a ferroptosis and iron-metabolism related lncRNA signature in lung adenocarcinoma

et al. 2021

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Background Long non-coding RNAs (lncRNAs) are increasingly recognized as the crucial mediators in the regulation of ferroptosis and iron metabolism. A systematic understanding of ferroptosis and iron-metabolism related lncRNAs (FIRLs) in lung adenocarcinoma (LUAD) is essential for new diagnostic and therapeutic strategies. Methods FIRLs were obtained through Pearson correlation analysis between ferroptosis and iron-metabolism related genes and all lncRNAs. Univariate and multivariate Cox regression analysis were used to identify optimal prognostic lncRNAs. Next, a novel signature was constructed and risk score of each patient was calculated. Survival analysis and ROC analysis were performed to evaluate the predictive performance using The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) and Gene Expression Omnibus (GEO) datasets, respectively. Furthermore, multivariate Cox and stratification analysis were used to assess prognostic value of this signature in whole cohort and various subgroups. The correlation of risk signature with immune infiltration and gene mutation was also discussed. The expression of lncRNAs was verified by quantitative real-time PCR (qRT-PCR). Results A 7-FIRLs signature including ARHGEF26-AS1, LINC01137, C20orf197, MGC32805, TMPO-AS1, LINC00324, and LINC01116 was established in the present study to assess the overall survival (OS) of LUAD. The survival analysis and ROC curve indicated good predictive performance of the signature in both the TCGA training set and the GEO validation set. Multivariate Cox and stratification analysis indicated that the 7‐FIRLs signature was an independent prognostic factor for OS. Nomogram exhibited robust validity in prognostic prediction. Differences in immune cells, immune functions and gene mutation were also found between high-risk and low-risk groups. Conclusions This risk signature based on the FIRLs may be promising for the clinical prediction of prognosis and immunotherapeutic responses in LUAD patients.

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Section: Methodsmentioning

confidence: 99%

Characterization of a ferroptosis and iron-metabolism related lncRNA signature in lung adenocarcinoma

et al. 2021

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“…We screened the FerrDb database ( http://www.zhounan.org/ferrdb/ ) and obtained 259 ferroptosis-related genes 13 . These genes were grouped and are shown in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

Chen

et al. 2021

Sci Rep

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Ovarian cancer (OV) is a common type of carcinoma in females. Many studies have reported that ferroptosis is associated with the prognosis of OV patients. However, the mechanism by which this occurs is not well understood. We utilized Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) to identify ferroptosis-related genes in OV. In the present study, we applied Cox regression analysis to select hub genes and used the least absolute shrinkage and selection operator to construct a prognosis prediction model with mRNA expression profiles and clinical data from TCGA. A series of analyses for this signature was performed in TCGA. We then verified the identified signature using International Cancer Genome Consortium (ICGC) data. After a series of analyses, we identified six hub genes (DNAJB6, RB1, VIMP/ SELENOS, STEAP3, BACH1, and ALOX12) that were then used to construct a model using a training data set. The model was then tested using a validation data set and was found to have high sensitivity and specificity. The identified ferroptosis-related hub genes might play a critical role in the mechanism of OV development. The gene signature we identified may be useful for future clinical applications.

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“…In order to make the coverage of this work aim at biological organism-derived compounds, as so-called “naturally occurring”, a natural product virtual library NPBS database was introduced in the used virtual screening method [ 36 ]. We imported all of the structures of natural products in NPBS and matched throughout with the MCSs described above to determine if the target natural product molecule contains maximum common substructure of reported AAAs.…”

Section: Methodsmentioning

confidence: 99%

“…Obtaining sufficient biological source information of a natural product used to be a profound investigation, given that the same natural product and its homologues can originate from various biological sources reported by multiple biomolecule-extracting research projects [ 36 ]. Thanks to the data resources of biological and chemical information, there is no need to peruse all of the related publications to search biological sources of a specific natural product.…”

Section: Introductionmentioning

confidence: 99%

Computational Analysis of Naturally Occurring Aristolochic Acid Analogues and Their Biological Sources

Chen

Zhou

et al. 2021

Biomolecules

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Aristolochic acids are known for nephrotoxicity, and implicated in multiple cancer types such as hepatocellular carcinomas demonstrated by recent studies. Natural products that are analogues to aristolochic acids have been constantly isolated from organisms; a larger chemical space of these compounds and a wider coverage of biological sources should be determined in consideration of the potential hazard of aristolochic acid analogues and the wide distribution of their biological sources in the nature. Therefore, we carried out an in silico research of naturally occurring aristolochic acid analogues and their biological sources, as a supplement to existing studies. The result shows a chemical space of 238 naturally occurring aristolochic acid analogues that are present in 175 species of biological sources including 44 traditional medicines. With the computational estimation for toxicity and the implication in hazard assessment of a biological source with the presence of aristolochic acid analogues, we propose that additional awareness should be raised to the public for avoidance of toxic species, especially those that are used as herbal medicines and easily accessible.

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NPBS database: a chemical data resource with relational data between natural products and biological sources

Cited by 19 publications

References 24 publications

Characterization of a ferroptosis and iron-metabolism related lncRNA signature in lung adenocarcinoma

Characterization of a ferroptosis and iron-metabolism related lncRNA signature in lung adenocarcinoma

A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma

Computational Analysis of Naturally Occurring Aristolochic Acid Analogues and Their Biological Sources

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