ArticleMolecular cell2017
Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.
Article in Molecular cell, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Time-resolved functional genomics using deep learning reveals global hierarchical control of autophagy.Nature cell biology · 2026Article
- Using Biological Networks to Guide Biomedical Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences.Molecular genetics and genomics : MGG · 2024Article
- Interpretation of cancer mutations using a multiscale map of protein systems.Science (New York, N.Y.) · 2021Article
- Mapping the multiscale structure of biological systems.Cell systems · 2021Review
- Environmental robustness of the global yeast genetic interaction network.Science (New York, N.Y.) · 2021Article
- On the relevance of precision autophagy flux controlAutophagy · 2020Article
- A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli.Bioinformatics (Oxford, England) · 2020Article
- Article
- IdentifyingFrontiers in genetics · 2020Article
- The great hairball gambit.PLoS genetics · 2019Article
- Gyp1 has a dual function as Ypt1 GAP and interaction partner of Atg8 in selective autophagy.Autophagy · 2019Article
- Article
- Review
- Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy.Disease models & mechanisms · 2019Article
- Review
- Lipid trafficking by yeast Snx4 family SNX-BAR proteins promotes autophagy and vacuole membrane fusion.Molecular biology of the cell · 2018Article
- Article
- The LRRK2 signalling system.Cell and tissue research · 2018Review
- Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping.Molecular cell · 2018Article
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Authors and funding
12 authors.
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Abstract
We have developed a general progressive procedure, Active Interaction Mapping, to guide assembly of the hierarchy of functions encoding any biological system. Using this process, we assemble an ontology of functions comprising autophagy, a central recycling process implicated in numerous diseases. A first-generation model, built from existing gene networks in Saccharomyces, captures most known autophagy components in broad relation to vesicle transport, cell cycle, and stress response. Systematic analysis identifies synthetic-lethal interactions as most informative for further experiments; consequently, we saturate the model with 156,364 such measurements across autophagy-activating conditions. These targeted interactions provide more information about autophagy than all previous datasets, producing a second-generation ontology of 220 functions. Approximately half are previously unknown; we confirm roles for Gyp1 at the phagophore-assembly site, Atg24 in cargo engulfment, Atg26 in cytoplasm-to-vacuole targeting, and Ssd1, Did4, and others in selective and non-selective autophagy. The procedure and autophagy hierarchy are at http://atgo.ucsd.edu/.
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