AIMC Topic: Gene Ontology
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Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
Open biology
Sep 2, 2020
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionall...
Construction of gene-classifier and co-expression network analysis of genes in association with major depressive disorder.
Psychiatry research
Aug 13, 2020
Because the pathogenesis of major depressive disorder (MDD) is still unclear and the accurate diagnosis remains unavailable, we aimed to analyze its molecular mechanisms and develop a gene classifier to improve diagnostic accuracy. We extracted diffe...
A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data.
Genes
Aug 12, 2020
DNA methylation change has been useful for cancer biomarker discovery, classification, and potential treatment development. So far, existing methods use either differentially methylated CpG sites or combined CpG sites, namely differentially methylate...
Using an ontology of the human cardiovascular system to improve the classification of histological images.
Scientific reports
Jul 23, 2020
The advantages of automatically recognition of fundamental tissues using computer vision techniques are well known, but one of its main limitations is that sometimes it is not possible to classify correctly an image because the visual information is ...
Association study based on topological constraints of protein-protein interaction networks.
Scientific reports
Jul 1, 2020
The non-random interaction pattern of a protein-protein interaction network (PIN) is biologically informative, but its potentials have not been fully utilized in omics studies. Here, we propose a network-permutation-based association study (NetPAS) m...
Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment.
Journal of integrative bioinformatics
Jun 29, 2020
To date, many proteins generated by large-scale genome sequencing projects are still uncharacterized and subject to intensive investigations by both experimental and computational means. Knowledge of protein subcellular localization (SCL) is of key i...
Predicting protein subcellular location with network embedding and enrichment features.
Biochimica et biophysica acta. Proteins and proteomics
Jun 25, 2020
The subcellular location of a protein is highly related to its function. Identifying the location of a given protein is an essential step for investigating its related problems. Traditional experimental methods can produce solid determination. Howeve...
Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes.
PloS one
Jun 19, 2020
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds-related FNTDC...
Identification of feature risk pathways of smoking-induced lung cancer based on SVM.
PloS one
Jun 4, 2020
OBJECTIVE: The present study aims to explore the role of smoking factors in the risk of lung cancer and screen the feature risk pathways of smoking-induced lung cancer.
Using Reactome to build an autophagy mechanism knowledgebase.
Autophagy
Jun 2, 2020
The 21st century has revealed much about the fundamental cellular process of autophagy. Autophagy controls the catabolism and recycling of various cellular components both as a constitutive process and as a response to stress and foreign material inv...
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