Exploring autophagy with Gene Ontology

Abstract

Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study.

Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson’s disease heritability

“…To address this question, we applied stratified LDSC to gene sets implicated in PD by Mendelian forms of PD, functional assays performed in the context of PD-associated mutations, such as the A53T missense mutation in SNCA, and rare-variant studies of sporadic PD [25][26][27][28][29][30] . In particular, we focused on gene sets associated with autophagy 26,27 , the lysosomal system 28 and mitochondrial function 29,30 .…”

“…We investigated three gene sets with previous biological support for involvement in PD: autophagy, lysosomal and mitochondrial [25][26][27][28][29][30] . The autophagy gene set included all genes associated with the Gene Ontology terms: GO:0006914 ("autophagy") and GO:0005776 ("autophagosome"), as derived from the GO C5 collection of the MSigDB database (v5.2).…”

Resources to Discover and Use Short Linear Motifs in Viral Proteins

“…Modulating autophagy is an example of recent advances in this research area [33,34]. A growing number of reports describe how virus proteins and SLiMs therein modulate autophagy to promote various aspects of their life cycle [34,35].…”

“…Blue arrows indicate 'part of' relations, which relate to the symbiont process as parts to a whole. autophagy processes, including positive and negative regulation of xenophagy, the selective autophagy of pathogens [33][34][35].…”

Mechanical loading mitigates osteoarthritis symptoms by regulating endoplasmic reticulum stress and autophagy

“…Autophagy is a major catabolic process of eukaryotic cells that degrades and recycles damaged macromolecules and organelles (29,30). In cartilage homeostasis, its activation is reported to reduce OA severity (31,32).…”