InterMineR: an R package for InterMine databases

Kyritsis, Konstantinos; Wang, Bing; Sullivan, Julie; Lyne, Rachel; Micklem, Gos

doi:10.1093/bioinformatics/btz039

Cited by 20 publications

(17 citation statements)

References 6 publications

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“…Significance of GO terms were assessed using permutation testing (10,000 iterations), where, in each permutation, the association between subjects and diets were randomised. Disease processes associated with gene preferential expression were determined using the Mouse Genome Informatics (MGI) database 46 , 47 . Human disease terms containing fewer than 15 homologous mouse genes were excluded from the analysis (leaving 13 disease terms in all).…”

Section: Methodsmentioning

confidence: 99%

Exposure to maternal high-fat diet induces extensive changes in the brain of adult offspring

et al. 2021

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Maternal environmental exposures, such as high-fat diets, diabetes and obesity, can induce long-term effects in offspring. These effects include increased risk of neurodevelopmental disorders (NDDs) including autism spectrum disorder (ASD), depression and anxiety. The mechanisms underlying these late-life neurologic effects are unknown. In this article, we measured changes in the offspring brain and determined which brain regions are sensitive to maternal metabolic milieu and therefore may mediate NDD risk. We showed that mice exposed to a maternal high-fat diet display extensive brain changes in adulthood despite being switched to a low-fat diet at weaning. Brain regions impacted by early-life diet include the extended amygdalar system, which plays an important role in reward-seeking behaviour. Genes preferentially expressed in these regions have functions related to feeding behaviour, while also being implicated in human NDDs, such as autism. Our data demonstrated that exposure to maternal high-fat diet in early-life leads to brain alterations that persist into adulthood, even after dietary modifications.

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Section: Methodsmentioning

confidence: 99%

Exposure to maternal high-fat diet induces extensive changes in the brain of adult offspring

et al. 2021

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“…To this end, data mining was performed from dbSNP database using reutils [ 19 , 20 ]. In addition, further information on genes, associated with the selected SNPs through GWAS, were retrieved from HumanMine database [ 21 ] using InterMineR [ 22 ]. Our approach led to the formation of a list with 127 genes that have been associated with the selected SNPs.…”

Section: Methodsmentioning

confidence: 99%

The GEnetic Syntax Score: a genetic risk assessment implementation tool grading the complexity of coronary artery disease—rationale and design of the GESS study

Vizirianakis

Chatzopoulou

Papazoglou

et al. 2021

BMC Cardiovasc Disord

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Background Coronary artery disease (CAD) remains one of the leading causes of mortality worldwide and is associated with multiple inherited and environmental risk factors. This study is designed to identify, design, and develop a panel of genetic markers that combined with clinical and angiographic information, will facilitate the creation of a personalized risk prediction algorithm (GEnetic Syntax Score—GESS). GESS score could be a reliable tool for predicting cardiovascular risk for future adverse events and for guiding therapeutic strategies. Methods GESS (ClinicalTrials.gov Identifier: NCT03150680) is a prospective, non-interventional clinical study designed to enroll 1080 consecutive patients with no prior history of coronary revascularization procedure, who undergo scheduled or emergency coronary angiography in AHEPA, University General Hospital of Thessaloniki. Next generation sequencing (NGS) technology will be used to genotype specific single-nucleotide polymorphisms (SNPs) across the genome of study participants, which were identified as clinically relevant to CAD after extensive bioinformatic analysis of literature-based SNPs. Enrichment analyses of Gene Ontology-Molecular Function, Reactome Pathways and Disease Ontology terms were also performed to identify the top 15 statistically significant terms and pathways. Furthermore, the SYNTAX score will be calculated for the assessment of CAD severity of all patients based on their angiographic findings. All patients will be followed-up for one-year, in order to record any major adverse cardiovascular events. Discussion A group of 228 SNPs was identified through bioinformatic and pharmacogenomic analysis to be involved in CAD through a wide range of pathways and was correlated with various laboratory and clinical parameters, along with the patients' response to clopidogrel and statin therapy. The annotation of these SNPs revealed 127 genes being affected by the presence of one or more SNPs. The first patient was enrolled in the study in February 2019 and enrollment is expected to be completed until June 2021. Hence, GESS is the first trial to date aspiring to develop a novel risk prediction algorithm, the GEnetic Syntax Score, able to identify patients at high risk for complex CAD based on their molecular signature profile and ultimately promote pharmacogenomics and precision medicine in routine clinical settings. Trial registration GESS trial registration: ClinicalTrials.gov Number: NCT03150680. Registered 12 May 2017- Prospectively registered, https://clinicaltrials.gov/ct2/show/NCT03150680.

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“…Functional enrichment analysis of significantly differentially expressed genes were performed using the Kyoto Encyclopaedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/) and REACTOME (http://reactome.org) databases, implemented using the Intermine R library and the humanmine database (44)(45). KEGG and REACTOME enriched terms were selected using a false discovery rate threshold of 0.05 (Holm-Bonferroni correction).…”

Section: Methodsmentioning

confidence: 99%

ILF3 contributes to the establishment of the antiviral type I interferon program

Watson

Bellora

Macías

2019

Preprint

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Upon detection of viral infections, cells activate the expression of type I interferons (IFNs) and pro-inflammatory cytokines to control viral dissemination. As part of their antiviral response, cells also trigger the translational shutoff response which prevents translation of viral mRNAs and cellular mRNAs in a non-selective manner. Intriguingly, mRNAs encoding for antiviral factors bypass this translational shutoff, suggesting the presence of additional regulatory mechanisms enabling expression of the self-defence genes. Here, we identified the dsRNA binding protein ILF3 as an essential host factor required for efficient translation of the central antiviral cytokine, IFNB1, and a subset of interferon-stimulated genes. By combining polysome profiling and next-generation sequencing, ILF3 was also found to be necessary to establish the dsRNA-induced transcriptional and translational programs. We propose a central role for the host factor ILF3 in enhancing expression of the antiviral defence mRNAs in cellular conditions where cap-dependent translation is compromised.

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InterMineR: an R package for InterMine databases

Cited by 20 publications

References 6 publications

Exposure to maternal high-fat diet induces extensive changes in the brain of adult offspring

Exposure to maternal high-fat diet induces extensive changes in the brain of adult offspring

The GEnetic Syntax Score: a genetic risk assessment implementation tool grading the complexity of coronary artery disease—rationale and design of the GESS study

ILF3 contributes to the establishment of the antiviral type I interferon program

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