Event Ontology: A Pathway-Centric Ontology for Biological Processes

Kim

Toxicol. Environ. Health Sci.

et al. 2011

Polycyclic aromatic hydrocarbons (PAHs) are ubiquious in the environment both as natural products and as environmental contaminants. Among PAHs, phenanthrene (PH) that is ubiquitously distributed throughout the environment was subjected in this study. Although environmental distribution and metabolism of PH have been well reported, there are only a few studies examined the expression of mRNA and their functions on PH-induced toxicity. A new paradigm in toxicity screening, toxicogenomic technology represents a useful approach for evaluating the toxic properties of environmental pollutants. In this respect, we elicited the genes which were changed more than 2-fold by analysis of gene expression profiles in human hepatocellular carcinoma (HepG2) cells, exposed to PH by using human oligonucleotide chip. 913 up-and 814 down-regulated genes changed their expression by more than 2-fold and p-values 0.05 through PH exposure. Gene Ontology (GO) analysis on these genes revealed significant enrichments in the several key biological processes related to the hepatotoxicity such as cell migration, wound healing, cytoskeleton organization, microtubule-based process, apoptosis, and cell cycle checkpoint. In conclusion, the present study suggests that PH exerts its toxicity by modulating the mRNA expression in HepG2 cells. we suggest that genes expressed by PH as a molecular signature which can be used more widely implemented in combination with more traditional techniques for assessment and prediction of toxicity by exposure to PH.

Section: Gene Expression Analysis Identifies Potential Biomarkers Of mentioning

confidence: 99%

mentioning

confidence: 99%

Gene expression analysis identifies potential biomarkers of phenanthrene in human hepatocytes (HepG2)

Kim

Toxicol. Environ. Health Sci.

et al. 2011

Expert Opinion on Drug Safety

“…Gene Ontology is generally used to annotate the functions of genes and is composed of three domains: biological processes, cellular components and molecular functions. However, it does not deal with the relationships between pathways and sub-pathways or between pathways and their related biological phenomena [71]. Thus, the association of the Kyoto Encyclopaedia of Genes and Genomes (KEGG) containing information on biological pathways and GO is useful for analyzing the function of genes.…”

Section: Expert Opinionmentioning

confidence: 99%

Mechanisms underlying methotrexate-induced pulmonary toxicity

Kim

Song²,

Ryu³

2009

The mechanisms underlying MTX toxicity are complex. The clinical effects may be attributable to both the anti-inflammatory and immunosuppressive effects of MTX. The mechanisms causing the side effects of MTX include mutation of the genotype, inhibition of transport, MTX-polyglutamates and P-glycoprotein binding with MTX. The p38 MAPK-signaling pathway is especially associated with a pulmonary inflammatory response. These mechanisms can be applied to optimize drug treatment.

Proceedings of the 1st International Workshop on Text Mining in Bioinformatics

“…PSI-MOD is partly constructed using RESID [15] terms, a controlled vocabulary for defining modification features of protein entries in the UniProt Knowledgebase (UniProtKB) [12]. PSI-MI [17] and INOH Event Ontology (EO) [22] are ontologies that, in part, describe the events of protein interaction. Finally, the Molecule Role Ontology [38], another ontology developed for INOH pathway (http://www.inoh.org/) curation, contains molecular functional group names, abstract molecule names and concrete molecule names manually collected from literature.…”

Section: Other Protein-related Ontologiesmentioning

confidence: 99%

Framework for a protein ontology

Natale

Arighi

Barker

et al. 2006

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies-one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir.georgetown.edu/pro).