Table 1.
Currently available autophagy-related resources.
| Database | URL | Description | References |
|---|---|---|---|
| Autophagy Regulation Network | http://autophagyregulation.org/ | Autophagy core proteins and their regulators with experimentally verified and predicted interactions in human. | Türei et al., 2015 |
| The Human Autophagy Database | http://autophagy.lu/ | Manually curation of autophagy proteins and their regulators. | |
| The Autophagy Database | http://www.tanpaku.org/autophagy/ | Provides information about proteins related to autophagy, including protein structure data in 41 species. | Homma et al., 2011 |
| The Autophagy Ontology | http://atgo.ucsd.edu/ | Ontology of functions related to autophagy, explains and presents the hierarchy of functions in autophagy in yeast and human. | Kramer et al., 2017 |
| ELM | http://elm.eu.org | Annotation and detection of eukaryotic linear motifs (ELMs). | Gouw et al., 2017 |
| Gerontology-Autophagic-MicroRNA Database | http://gamdb.liu-lab.com/index.php | Experimentally validated interactions between miRNA and genes or proteins in gerontology-related disorders manually curated from the literature focusing on autophagy. | Zhang et al., 2016 |
| hfAIM | http://bioinformatics.psb.ugent.be/hfAIM/ | Identification of LIR/AIM motifs in protein sequences | Xie et al., 2016 |
| iLIR | http://repeat.biol.ucy.ac.cy/iLIR | Identification of LIR/AIM motifs in protein sequences and providing a PSSM score indicating the significance of the hits. | Kalvari et al., 2014 |
| iLIR database | http://ilir.uk/model | A database listing all the putative LIR-containing proteins from 8 model organisms; GO analysis. | Jacomin et al., 2016 |
| iLIR@viral | http://ilir.uk/virus/ | Database of all the putative LIR-containing proteins in viruses. | Jacomin et al., 2017 |
| ncRDeathDB | http://www.rna-society.org/ncrdeathdb | Collection of programmed cell death associated non-coding RNAs (including microRNA, long noncoding RNA/lncRNA and small nucleolar RNA/snoRNA). | Wu et al., 2015 |
| SLiMSearch | http://slim.ucd.ie/ slimsearch/ | Search function in given protein(s) for a specific consensus motif for the discovery of novel motif instances. | Krystkowiak and Davey, 2017 |
| THANATOS | http://thanatos.biocuckoo.org/ | Manually curated collection of experimentally verified regulators during programmed cell death in eukaryotes. | Deng et al., 2018 |