Exploring autophagy with Gene Ontology

被引:117
作者
Denny, Paul [1 ,5 ]
Feuermann, Marc [2 ]
Hill, David P. [3 ,6 ]
Lovering, Ruth C. [1 ]
Plun-Favreau, Helene [4 ]
Roncaglia, Paola [5 ,6 ]
机构
[1] UCL, Inst Cardiovasc Sci, Funct Gene Annotat, London, England
[2] SIB Swiss Inst Bioinformat, Geneva, Switzerland
[3] Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA
[4] UCL Inst Neurol, Dept Mol Neurosci, London, England
[5] European Mol Biol Lab, European Bioinformat Inst EMBL EBI, Wellcome Genome Campus, Cambridge, England
[6] Gene Ontol Consortium, Cambridge, England
基金
美国国家卫生研究院;
关键词
annotation; autophagy; biocuration; curation; enrichment analysis; Gene Ontology; network analysis; Parkinson disease; PARKINSONS-DISEASE; FOAM CELLS; BECLIN; MECHANISMS; RESOURCE; DATABASE; MICROAUTOPHAGY; MITOPHAGY; PROTEINS; ACTIVATION;
D O I
10.1080/15548627.2017.1415189
中图分类号
Q2 [细胞生物学];
学科分类号
071013 [干细胞生物学];
摘要
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.
引用
收藏
页码:419 / 436
页数:18
相关论文
共 106 条
[1]
[Anonymous], PATHW VIEW PARK DIS
[2]
[Anonymous], SOFTW DOWNL AV GITH
[3]
[Anonymous], SOFTW TOOL US ED GEN
[4]
[Anonymous], GEN ONT TERM ANN BRO
[5]
[Anonymous], ANN FIL ALL ARCH FOL
[6]
[Anonymous], PANTHER PROT AN EV R
[7]
[Anonymous], INF CONTR ANN COMM G
[8]
[Anonymous], ONT FIL ALL ARCH CUR
[9]
[Anonymous], GEN ONT EV COD DOC 2
[10]
[Anonymous], GEN ONT TERM ANN BRO