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Autophagy dark genes: Can we find them with machine learning?

https://doi.org/10.1101/715037
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/path.2094openalex-snapshot
Autophagy, organelles and ageing
inferredcites →https://doi.org/10.1002/prot.21989openalex-snapshot
An integrated approach to inferring gene–disease associations in humans
inferredcites →https://doi.org/10.1007/978-3-319-42007-3_26openalex-snapshot
S-Rank: A Supervised Ranking Framework for Relationship Prediction in Heterogeneous Information Networks
inferredcites →https://doi.org/10.1007/s00335-012-9422-2openalex-snapshot
The mammalian gene function resource: the international knockout mouse consortium
inferredcites →https://doi.org/10.1007/s00335-019-09809-0openalex-snapshot
Exploring the dark genome: implications for precision medicine
inferredcites →https://doi.org/10.1007/s10522-017-9683-yopenalex-snapshot
A review of supervised machine learning applied to ageing research
inferredcites →https://doi.org/10.1016/j.ceb.2009.11.014openalex-snapshot
Mammalian autophagy: core molecular machinery and signaling regulation
inferredcites →https://doi.org/10.1016/j.cell.2012.11.001openalex-snapshot
The Hairpin-type Tail-Anchored SNARE Syntaxin 17 Targets to Autophagosomes for Fusion with Endosomes/Lysosomes
inferredcites →https://doi.org/10.1016/j.cell.2018.09.048openalex-snapshot
Biological Functions of Autophagy Genes: A Disease Perspective
inferredcites →https://doi.org/10.1016/j.cels.2019.06.005openalex-snapshot
A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines
inferredcites →https://doi.org/10.1016/j.febslet.2010.02.054openalex-snapshot
The role of PI3P phosphatases in the regulation of autophagy
inferredcites →https://doi.org/10.1016/j.molcel.2010.09.023openalex-snapshot
Autophagy and the Integrated Stress Response
inferredcites →https://doi.org/10.1016/j.molcel.2016.08.021openalex-snapshot
The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Determines the Fusion Specificity of Autophagosomes with Late Endosomes/Lysosomes
inferredcites →https://doi.org/10.1016/j.nbd.2015.03.002openalex-snapshot
Redox regulation of autophagy in healthy brain and neurodegeneration
inferredcites →https://doi.org/10.1016/j.ymeth.2014.11.020openalex-snapshot
DISEASES: Text mining and data integration of disease–gene associations
inferredcites →https://doi.org/10.1017/s1462399409001306openalex-snapshot
The role of autophagy in tumour development and cancer therapy
inferredcites →https://doi.org/10.1038/aps.2010.118openalex-snapshot
Autophagic pathways as new targets for cancer drug development
inferredcites →https://doi.org/10.1038/cdd.2008.126openalex-snapshot
Autophagy genes and ageing
inferredcites →https://doi.org/10.1038/labinvest.2014.131openalex-snapshot
Regulation of autophagy by protein post-translational modification
inferredcites →https://doi.org/10.1038/nature06639openalex-snapshot
Autophagy fights disease through cellular self-digestion
inferredcites →https://doi.org/10.1038/nature11003openalex-snapshot
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
inferredcites →https://doi.org/10.1038/nature11910openalex-snapshot
Autophagosomes form at ER–mitochondria contact sites
inferredcites →https://doi.org/10.1038/ncb2152openalex-snapshot
AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1
inferredcites →https://doi.org/10.1038/nrd.2018.52openalex-snapshot
Erratum: Unexplored therapeutic opportunities in the human genome
inferredcites →https://doi.org/10.1074/jbc.m706956200openalex-snapshot
The Pancreatitis-induced Vacuole Membrane Protein 1 Triggers Autophagy in Mammalian Cells
inferredcites →https://doi.org/10.1074/jbc.ra118.002527openalex-snapshot
MAPK15 is part of the ULK complex and controls its activity to regulate early phases of the autophagic process
inferredcites →https://doi.org/10.1083/jcb.200712064openalex-snapshot
FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells
inferredcites →https://doi.org/10.1083/jcb.201804132openalex-snapshot
Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation
inferredcites →https://doi.org/10.1093/bioinformatics/btq466openalex-snapshot
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
inferredcites →https://doi.org/10.1093/database/bav006openalex-snapshot
PathCards: multi-source consolidation of human biological pathways
inferredcites →https://doi.org/10.1093/nar/gkq906openalex-snapshot
ChemProt: a disease chemical biology database
inferredcites →https://doi.org/10.1093/nar/gkq995openalex-snapshot
The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/nar/gku1026openalex-snapshot
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease
inferredcites →https://doi.org/10.1093/nar/gku1203openalex-snapshot
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
inferredcites →https://doi.org/10.1093/nar/gkv1222openalex-snapshot
ClinVar: public archive of interpretations of clinically relevant variants
inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot
The Reactome pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkw1072openalex-snapshot
Pharos: Collating protein information to shed light on the druggable genome
inferredcites →https://doi.org/10.1093/nar/gkw1092openalex-snapshot
KEGG: new perspectives on genomes, pathways, diseases and drugs
inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkw1107openalex-snapshot
InterPro in 2017—beyond protein family and domain annotations
inferredcites →https://doi.org/10.1093/nar/gkw1108openalex-snapshot
Expansion of the Gene Ontology knowledgebase and resources
inferredcites →https://doi.org/10.1093/nar/gkw937openalex-snapshot
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
inferredcites →https://doi.org/10.1093/nar/gky458openalex-snapshot
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks
inferredcites →https://doi.org/10.1109/asonam.2011.112openalex-snapshot
Co-author Relationship Prediction in Heterogeneous Bibliographic Networks
inferredcites →https://doi.org/10.1109/tst.2015.7297749openalex-snapshot
Computational approaches for prioritizing candidate disease genes based on PPI networks
inferredcites →https://doi.org/10.1126/science.1260419openalex-snapshot
Tissue-based map of the human proteome
inferredcites →https://doi.org/10.1128/jvi.02383-15openalex-snapshot
Knockdown of Autophagy Inhibits Infectious Hepatitis C Virus Release by the Exosomal Pathway
inferredcites →https://doi.org/10.1145/2124295.2124373openalex-snapshot
When will it happen?
inferredcites →https://doi.org/10.1145/2939672.2939785openalex-snapshot
XGBoost
inferredcites →https://doi.org/10.1146/annurev-cellbio-092910-154005openalex-snapshot
The Role of Atg Proteins in Autophagosome Formation
inferredcites →https://doi.org/10.1155/2012/219625openalex-snapshot
Autophagy: More Than a Nonselective Pathway
inferredcites →https://doi.org/10.1155/2014/603980openalex-snapshot
Tumor Suppression and Promotion by Autophagy
inferredcites →https://doi.org/10.1186/1471-2105-12-389openalex-snapshot
ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples
inferredcites →https://doi.org/10.1186/s12859-016-1005-xopenalex-snapshot
Predicting drug target interactions using meta-path-based semantic network analysis
inferredcites →https://doi.org/10.1186/s13326-017-0161-xopenalex-snapshot
Drug target ontology to classify and integrate drug discovery data
inferredcites →https://doi.org/10.1258/ebm.2011.010360openalex-snapshot
The emerging role of autophagy in alcoholic liver disease
inferredcites →https://doi.org/10.1371/journal.pbio.2007044openalex-snapshot
CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor
inferredcites →https://doi.org/10.1371/journal.pcbi.1004259openalex-snapshot
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
inferredcites →https://doi.org/10.1371/journal.pgen.1006423openalex-snapshot
Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues
inferredcites →https://doi.org/10.1371/journal.pone.0065390openalex-snapshot
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
inferredcites →https://doi.org/10.1371/journal.pone.0097079openalex-snapshot
Ensemble Positive Unlabeled Learning for Disease Gene Identification
inferredcites →https://doi.org/10.15252/embr.201845889openalex-snapshot
TMEM41B is a novel regulator of autophagy and lipid mobilization
inferredcites →https://doi.org/10.18632/aging.101264openalex-snapshot
Machine learning for predicting lifespan-extending chemical compounds
inferredcites →https://doi.org/10.18632/oncotarget.3523openalex-snapshot
MicroRNAs in apoptosis, autophagy and necroptosis
inferredcites →https://doi.org/10.3389/fimmu.2012.00043openalex-snapshot
Autophagosomal Protein Dynamics and Influenza Virus Infection
inferredcites →https://doi.org/10.3389/fnmol.2017.00170openalex-snapshot
Autophagy and Its Impact on Neurodegenerative Diseases: New Roles for TDP-43 and C9orf72
inferredcites →https://doi.org/10.3390/ijms18020367openalex-snapshot
Role of Autophagy and Apoptosis in Non-Small-Cell Lung Cancer
inferredcites →https://doi.org/10.3390/ijms18102036openalex-snapshot
Proteome Stability as a Key Factor of Genome Integrity
inferredcites →https://doi.org/10.4161/auto.21857openalex-snapshot
MAPK15/ERK8 stimulates autophagy by interacting with LC3 and GABARAP proteins
inferredcites →https://doi.org/10.4161/auto.26864openalex-snapshot
Characterization of early autophagy signaling by quantitative phosphoproteomics
inferredcites →https://doi.org/10.4161/auto.3636openalex-snapshot
Autophagy Regulates Ageing inC. elegans
inferredcites →https://doi.org/10.4161/auto.5.7.9296openalex-snapshot
Atg101, a novel mammalian autophagy protein interacting with Atg13
inferredcites →https://doi.org/10.4161/auto.6.4.12244openalex-snapshot
A comprehensive glossary of autophagy-related molecules and processes
inferredcites →https://doi.org/10.4161/auto.7.11.17661openalex-snapshot
A comprehensive glossary of autophagy-related molecules and processes (2ndedition)
inferredcites →https://doi.org/10.5402/2012/738718openalex-snapshot
Autophagy: New Questions from Recent Answers

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ntls.20220067openalex-snapshot
Autophagy dark genes: Can we find them with machine learning?
inferred← citeshttps://doi.org/10.1016/j.bbadis.2024.167263openalex-snapshot
Autophagy and machine learning: Unanswered questions
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00431openalex-snapshot
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
inferred← citeshttps://doi.org/10.1039/d0cs01065kopenalex-snapshot
A critical overview of computational approaches employed for COVID-19 drug discovery
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