“…In the functional enrichment, the DEGs were mainly enriched in negative regulation of phosphate metabolic process and positive regulation of cell cycle process gene ontologies (GOs); the enriched pathways were the phosphoinositide 3-kinase-serine/threonine kinase signaling pathway, bladder cancer, and microRNAs in cancer. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The classification pattern that underlies these systems provides a good case study of the move toward formalization in part because it illustrates some of the barriers to formalization, including the formal complexity of the pattern and the ontological issues surrounding the “one and the many.” …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…To explore how FUS mutations impinge on motor neuron-specific RNA-based circuitries, we performed transcriptome profiling of small and long RNAs of motor neurons (MNs) derived from mouse embryonic stem cells carrying a FUS-P517L knock-in mutation, which is equivalent to human FUS-P525L, associated with a severe and juvenile-onset form of ALS. Combining ontological, predictive and molecular analyses, we found an inverse correlation between several classes of deregulated miRNAs and their corresponding mRNA targets in both homozygous and heterozygous P517L MNs. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Moreover, this approach can semantically enrich the measured connectivity of an individual subject by the semantic context from ontologies, brain atlases and molecular biological databases. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…However, there has yet to be an enrichment analysis of the shared ontologies and pathways of known ASD genes and lncRNAs in normal brain development. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Differentially expressed genes were normalized to control subjects without tuberculosis, and ontologically mapped to identify a spatially compartmentalized pathophysiological map of the cavity. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…FNS with normal facial nerve function may sometimes be misdiagnosed as otitis media because of similar ontological symptoms such as purulence, tympanic membrane damage, and hearing loss. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…In this article, we aim to develop an in silico multi-label classification approach to predict whether a substrate can specifically recognize one of the 13 categories of drug transporters ranging from ATP-binding cassette to solute carrier families using both structural fingerprints and chemical ontologies information of substrates. The data-driven network-based label space partition (NLSP) method was utilized to construct the model based on a hybrid of similarity-based feature by the integration of 2D fingerprint and semantic similarity. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…To evaluate candidate genes, we combined well‐established gene ontologies with bone transcriptome data to compute bone‐enrichment scores for all protein‐coding genes. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Cytoscape software was employed to construct gene ontologies, metabolic pathways and gene-gene interaction networks. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Based on their gene ontologies, these genes were related – among others – to gene transcription/translation and its regulation, to immune response and the nervous system in general. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…We found that the upregulated DEGs were enriched in KEGG and gene ontologies associated with ovarian cancer progression, female gamete association, otic vesicle development, regulation of chromosome segregation, and therapeutic failure. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Compared with the disease gene prediction without using the information from the KEGG pathways, this method has a better prediction performance on inferring breast cancer–associated genes, and the top predicted genes are better enriched on known breast cancer–associated gene ontologies. Finally, we performed a literature search on top predicted novel genes and found that most of them are supported by at least wet-lab experiments on cell lines. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Methods: Genetic analysis of resected human lung adenocarcinoma was correlated to clinical-pathological characteristics, gene ontologies, and single cell RNA sequencing (scRNASeq). …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The functional enrichment of 624 DEGs identified in the blood transcriptome of patients with PTB revealed major dysregulation of T cell-related ontologies and pathways (q ≤ 0.05). Of the 96 DEGs shared between transcriptome and immune cell types, 39 overlapped with TB meta-profiling genetic signatures, and their semantic similarity analysis with the remaining 57 genes, yielded 45 new candidate TB markers. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…Participants received a series of closed-ended and open-ended questions probing their reasoning about disease transmission, with a focus on causal mechanisms underlying disease contraction, transmission, treatment, and prevention; non-visible (internal) biological processes; and ontological frameworks regarding what kinds of entities viruses are. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…This system leverages semantics using concepts, properties, and axioms from existing ontologies. In addition, we used the publicly available US Centers for Disease Control and Prevention 500 Cities data set to perform multivariate analysis. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso

“…The 2 lists of natural compound-target proteins were analyzed by the STITCH software (http://stitch.embl.de/) to develop protein-compound and protein-protein interaction networks (PPINs). An ontological enrichment (GO) analysis was performed by the Clue GO plugin to evaluate the PPIN generated by STITCH; finally, the molecular docking to predict the mode underlying the anti-inflammatory effects. …”
Enlace del recurso
Enlace del recurso
Enlace del recurso