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Gene Ontology

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Safer chemicals using less animals: kick-off of the European ONTOX project.

Toxicology
The 3Rs concept, calling for replacement, reduction and refinement of animal experimentation, is receiving increasing attention around the world, and has found its way to legislation, in particular in the European Union. This is aligned by continuing...

Identification of potential genomic biomarkers for Parkinson's disease using data pooling of gene expression microarrays.

Biomarkers in medicine
In this study, we aimed to identify potential diagnostic biomarkers Parkinson's disease (PD) by exploring microarray gene expression data of PD patients. Differentially expressed genes associated with PD were screened from the GSE99039 dataset usin...

Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning.

International journal of molecular sciences
Experimental studies of and have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are esse...

Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data.

Nature communications
Transcriptomic atlases have improved our understanding of the correlations between gene-expression patterns and spatially varying properties of brain structure and function. Gene-category enrichment analysis (GCEA) is a common method to identify func...

Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations.

BMC bioinformatics
BACKGROUND: The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these high-level concepts into data-le...

RDmap: a map for exploring rare diseases.

Orphanet journal of rare diseases
BACKGROUND: The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians. A map for visualizing, locating and navigating rare diseases based o...

PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks.

PloS one
Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as eff...

Integrated analysis of multiple microarray studies to identify novel gene signatures in preeclampsia.

Placenta
INTRODUCTION: Preeclampsia (PE) is one of the major causes of maternal and fetal morbidity and mortality in pregnancy worldwide. However, the intrinsic molecular mechanisms underlying the pathogenesis of PE have not yet been fully elucidated.

Graph embeddings on gene ontology annotations for protein-protein interaction prediction.

BMC bioinformatics
BACKGROUND: Protein-protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations and disease-drug associations. ...