Exploration of association between EPHX1 and chronic obstructive pulmonary disease on the basis of combined data mining

Liu, An; Xia, Hesheng; Zhou, Ping; Liu, Hua

doi:10.4238/gmr.15028639

Cited by 4 publications

(3 citation statements)

References 34 publications

(44 reference statements)

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“…However, in the case of Caucasians, we did not identify any statistically significant associations. In contrast, studies of An L found that EPHX1 rs2234922 is not associated with COPD pathogenesis (OR = 1.01, P Z = 0.65) ( An et al, 2016b ). Lee J et al concluded that although a statistically significant correlation was not observed, the presence of EPHX1 rs2234922 correlated with reduced COPD risk, consistent with the theory that the GA genotype of EPHX1 can increase the detoxification ability of the EPHX1 enzyme ( Lee et al, 2011 ).…”

Section: Discussionmentioning

confidence: 97%

“…These results are consistent with the observations that EPHX1 rs1051740 mutations decrease EPHX1 enzyme activity leading to an increase in the risk of COPD. A previous meta-analysis of 19 studies published in 2016 by An L et al did not find any association between EPHX1 rs1051740 and COPD risk in Asians (OR = 0.92, P Z= 0.31) and Caucasians (OR = 1.01, P Z= 0.65) ( An et al, 2016b ). However, this study only used the allele model to pool analysis, which has greater limitations and needs further in-depth mining and research.…”

Section: Discussionmentioning

confidence: 98%

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EPHX1 and GSTP1 polymorphisms are associated with COPD risk: a systematic review and meta-analysis

et al. 2023

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Background: Chronic obstructive pulmonary disease (COPD) affects approximately 400 million people worldwide and is associated with high mortality and morbidity. The effect of EPHX1 and GSTP1 gene polymorphisms on COPD risk has not been fully characterized.Objective: To investigate the association of EPHX1 and GSTP1 gene polymorphisms with COPD risk.Methods: A systematic search was conducted on 9 databases to identify studies published in English and Chinese. The analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guidelines (PRISMA). The pooled OR and 95% CI were calculated to evaluate the association of EPHX1 and GSTP1 gene polymorphisms with COPD risk. The I2 test, Q test, Egger’s test, and Begg’s test were conducted to determine the level of heterogeneity and publication bias of the included studies.Results: In total, 857 articles were retrieved, among which 59 met the inclusion criteria. The EPHX1 rs1051740 polymorphism (homozygote, heterozygote, dominant, recessives, and allele model) was significantly associated with high risk of COPD risk. Subgroup analysis revealed that the EPHX1 rs1051740 polymorphism was significantly associated with COPD risk among Asians (homozygote, heterozygote, dominant, and allele model) and Caucasians (homozygote, dominant, recessives, and allele model). The EPHX1 rs2234922 polymorphism (heterozygote, dominant, and allele model) was significantly associated with a low risk of COPD. Subgroup analysis showed that the EPHX1 rs2234922 polymorphism (heterozygote, dominant, and allele model) was significantly associated with COPD risk among Asians. The GSTP1 rs1695 polymorphism (homozygote and recessives model) was significantly associated with COPD risk. Subgroup analysis showed that the GSTP1 rs1695 polymorphism (homozygote and recessives model) was significantly associated with COPD risk among Caucasians. The GSTP1 rs1138272 polymorphism (heterozygote and dominant model) was significantly associated with COPD risk. Subgroup analysis suggested that the GSTP1 rs1138272 polymorphism (heterozygote, dominant, and allele model) was significantly associated with COPD risk among Caucasians.Conclusion: The C allele in EPHX1 rs1051740 among Asians and the CC genotype among Caucasians may be risk factors for COPD. However, the GA genotype in EPHX1 rs2234922 may be a protective factor against COPD in Asians. The GG genotype in GSTP1 rs1695 and the TC genotype in GSTP1 rs1138272 may be risk factors for COPD, especially among Caucasians.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 98%

EPHX1 and GSTP1 polymorphisms are associated with COPD risk: a systematic review and meta-analysis

et al. 2023

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“…There is therefore a growing interest for scientists to extract automatically relevant information from these texts. Several informatics tools have been developed for gene interaction (Mallory et al ., 2016), gene-disease (An et al ., 2016), disease-drug (Bravo et al ., 2015) extraction from scientific and medical texts. Several community challenges for text-mining in biology have been organized to cross-evaluate these tools (Krallinger et al ., 2008; Ananiadou et al ., 2015; Huang and Lu, 2016).…”

Section: Introductionmentioning

confidence: 99%

OntoContext, a new python package for gene contextualization based on the annotation of biomedical texts

Bedhiafi

Thomas‐Vaslin

Elgaaïed

et al. 2022

Preprint

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MotivationThe automatic mining for bibliography exploitation in given contexts is a challenge according to the increasing number of scientific publications and new concepts. Several indexing systems were developed for biomedical literature. However, such systems have failed to produce contextualised research of genes and proteins and automatically group texts according to shared concepts. In this paper, we present OntoContext, a contextualization system crossing the use of biomedical ontologies to annotate texts containing terms related to cell populations, anatomical locations and diseases and to extract gene, RNA or protein names in these contexts.ResultsOntoContext, a new python package contains two modules. The “annot” module for “annotation” function, is based on combination of morphosyntactic labelling and exact matching and on dictionaries derived from the Cell Ontology, the UBERON Ontology (anatomical context), the Human Disease Ontology and geniatagger, (which contains particular tags for gene-related names). The “annot” output is used as input for the second module “crisscross” generating lists of gene-related names obtained by crossing annotations from the three mentioned ontologies. OntoContext showed better performances than NCBO Annotator after evaluation on two text corpuses. OntoContext is freely available in the pypi.Availabilityhttps://pypi.python.org/pypi/OntoContext and https://github.com/walidbedhiafi/OntoContext1.Contactadrien.six@sorbonne-universite.fr

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Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies

Liu

Ran

et al. 2022

Canadian Respiratory Journal

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Background. Last two decades, many association studies on genetic variants and chronic obstructive pulmonary disease (COPD) risk have been published. But results from different studies are inconsistent. Therefore, we performed this article to systematically evaluate results from previous meta-analyses and genome-wide association studies (GWASs). Material and Methods. Firstly, we retrieved meta-analyses in PubMed, Embase, and China National Knowledge Infrastructure and GWASs in PubMed and GWAS catalog on or before April 7th, 2022. Then, data were extracted and screened. Finally, two main methods—Venice criteria and false-positive report probability test—were used to evaluate significant associations. Results. As a result, eighty-eight meta-analyses and 5 GWASs were deemed eligible for inclusion. Fifty variants in 26 genes obtained from meta-analyses were significantly associated with COPD risk. Cumulative epidemiological evidence of an association was graded as strong for 10 variants in 8 genes (GSTM1, CHRNA, ADAM33, SP-D, TNF-α, VDBP, HMOX1, and HHIP), moderate for 6 variants in 5 genes (PI, GSTM1, ADAM33, TNF-α, and VDBP), and weak for 40 variants in 23 genes. Five variants in 4 genes showed convincing evidence of no association with COPD risk in meta-analyses. Additionally, 29 SNPs identified in GWASs were proved to be noteworthy based on the FPRP test. Conclusion. In summary, more than half (52.38%) of genetic variants reported in previous meta-analyses showed no association with COPD risk. However, 13 variants in 9 genes had moderate to strong evidence for an association. This article can serve as a useful reference for further studies.

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Exploration of association between EPHX1 and chronic obstructive pulmonary disease on the basis of combined data mining

Cited by 4 publications

References 34 publications

EPHX1 and GSTP1 polymorphisms are associated with COPD risk: a systematic review and meta-analysis

EPHX1 and GSTP1 polymorphisms are associated with COPD risk: a systematic review and meta-analysis

OntoContext, a new python package for gene contextualization based on the annotation of biomedical texts

Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies

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