AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation

References

• Yorimitsu T, Klionsky DJ. Autophagy: molecular machinery for self-eating. Cell Death Differ. 2005;12 Suppl 2:1542–1552. doi: 10.1038/sj.cdd.4401765
   PubMed Web of Science ®Google Scholar
• Yin Z, Pascual C, Klionsky DJ. Autophagy: machinery and regulation. Microb Cell. 2016;3(12):588–596. doi: 10.15698/mic2016.12.546
   PubMed Web of Science ®Google Scholar
• Ariosa AR, Klionsky DJ. Autophagy core machinery: overcoming spatial barriers in neurons. J Mol Med. 2016;94(11):1217–1227. doi: 10.1007/s00109-016-1461-9
   PubMed Web of Science ®Google Scholar
• Mancias JD, Kimmelman AC. Mechanisms of selective autophagy in normal physiology and cancer. J Mol Biol. 2016;428(9):1659–1680. doi: 10.1016/j.jmb.2016.02.027
   PubMed Web of Science ®Google Scholar
• Kim J, Kundu M, Viollet B, et al. AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat Cell Biol. 2011;13(2):132–141. doi: 10.1038/ncb2152
   PubMed Web of Science ®Google Scholar
• Wilkinson DS, Jariwala JS, Anderson E, et al. Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Mol Cell. 2015;57(1):55–68. doi: 10.1016/j.molcel.2014.11.019
   PubMed Web of Science ®Google Scholar
• Kocaturk NM, Gozuacik D. Crosstalk between mammalian autophagy and the ubiquitin-proteasome System. Front Cell Dev Biol. 2018;6:128. doi: 10.3389/fcell.2018.00128
   PubMed Web of Science ®Google Scholar
• Dossou AS, Basu A. The Emerging roles of mTORC1 in macromanaging autophagy. Cancers (Basel). 2019;11(10):11. doi: 10.3390/cancers11101422
   Web of Science ®Google Scholar
• Vellai T. How the amino acid leucine activates the key cell-growth regulator mTOR. Nature. 2021;596(7871):192–194. doi: 10.1038/d41586-021-01943-7
   PubMedGoogle Scholar
• Hornbeck PV, Chabra I, Kornhauser JM, et al. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics. 2004;4(6):1551–1561. doi: 10.1002/pmic.200300772
   PubMed Web of Science ®Google Scholar
• Minguez P, Letunic I, Parca L, et al. Ptmcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res. 2015;43(D1):D494–502. doi: 10.1093/nar/gku1081
   PubMed Web of Science ®Google Scholar
• Deng W, Ma L, Zhang Y, et al. THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy. 2018;14(2):296–310. doi: 10.1080/15548627.2017.1402990
   PubMed Web of Science ®Google Scholar
• Chen K, Yang D, Zhao F, et al. Autophagy and tumor database: ATdb, a novel database connecting autophagy and tumor. Database (Oxford). 2020;2020. doi: 10.1093/database/baaa052.
   Google Scholar
• Fisher DE, Carr CS, Parent LA, et al. TFEB has DNA-binding and oligomerization properties of a unique helix-loop-helix/leucine-zipper family. Genes Dev. 1991;5(12a):2342–2352. doi: 10.1101/gad.5.12a.2342
   PubMed Web of Science ®Google Scholar
• Di Malta C, Cinque L, Settembre C. Transcriptional regulation of autophagy: mechanisms and diseases. Front Cell Dev Biol. 2019;7:114. doi: 10.3389/fcell.2019.00114
   PubMed Web of Science ®Google Scholar
• Sengupta A, Molkentin JD, Yutzey KE. FoxO transcription factors promote autophagy in cardiomyocytes. J Biol Chem. 2009;284(41):28319–28331. doi: 10.1074/jbc.M109.024406
   PubMed Web of Science ®Google Scholar
• Garcia-Alonso L, Holland CH, Ibrahim MM, et al. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res. 2019;29(8):1363–1375. doi: 10.1101/gr.240663.118
   PubMed Web of Science ®Google Scholar
• Yevshin I, Sharipov R, Valeev T, et al. GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res. 2017;45(D1):D61–D67. doi: 10.1093/nar/gkw951
   PubMed Web of Science ®Google Scholar
• Liska O, Bohár B, Hidas A, et al. Tflink: an integrated gateway to access transcription factor-target gene interactions for multiple species. Database (Oxford). 2022;2022. doi: 10.1093/database/baac083.
   PubMed Web of Science ®Google Scholar
• Akkoc Y, Gozuacik D. MicroRNAs as major regulators of the autophagy pathway. Biochim Biophys Acta, Mol Cell Res. 2020;1867(5):118662. doi: 10.1016/j.bbamcr.2020.118662
   PubMed Web of Science ®Google Scholar
• Yang L, Wang H, Shen Q, et al. Long non-coding RNAs involved in autophagy regulation. Cell Death Dis. 2017;8(10):e3073. doi: 10.1038/cddis.2017.464
   PubMed Web of Science ®Google Scholar
• Agarwal V, Bell GW, Nam J-W, et al. Predicting effective microRNA target sites in mammalian mRnas. Elife. 2015;4:4. doi: 10.7554/eLife.05005
   Web of Science ®Google Scholar
• Fabregat A, Sidiropoulos K, Garapati P, et al. The Reactome pathway Knowledgebase. Nucleic Acids Res. 2016;44(D1):D481–7. doi: 10.1093/nar/gkv1351
   PubMed Web of Science ®Google Scholar
• Türei D, Valdeolivas A, Gul L, et al. Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis. Mol Syst Biol. 2021;17(3):17. doi: 10.15252/msb.20209923
   Web of Science ®Google Scholar
• Wang N-N, Dong J, Zhang L, et al. Hamdb: a database of human autophagy modulators with specific pathway and disease information. J Cheminform. 2018;10(1):34. doi: 10.1186/s13321-018-0289-4
   PubMedGoogle Scholar
• Homma K, Suzuki K, Sugawara H. The autophagy database: an all-inclusive information resource on autophagy that provides nourishment for research. Nucleic Acids Res. 2011;39(Database):D986–90. doi: 10.1093/nar/gkq995
   PubMedGoogle Scholar
• Türei D, Földvári-Nagy L, Fazekas D, et al. Autophagy regulatory network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. Autophagy. 2015;11:155–165. doi: 10.4161/15548627.2014.994346
   PubMed Web of Science ®Google Scholar
• Csabai L, Fazekas D, Kadlecsik T, et al. SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. Nucleic Acids Res. 2022;50(D1):D701–D709. doi: 10.1093/nar/gkab909
   PubMed Web of Science ®Google Scholar
• Breuer K, Foroushani AK, Laird MR, et al. InnateDB: systems biology of innate immunity and beyond–recent updates and continuing curation. Nucleic Acids Res. 2013;41:D1228–33. doi: 10.1093/nar/gks1147
   PubMed Web of Science ®Google Scholar
• Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA. 2006;12:192–197. doi: 10.1261/rna.2239606
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–29. doi: 10.1038/75556
   PubMed Web of Science ®Google Scholar
• Parzych KR, Klionsky DJ. An overview of autophagy: morphology, mechanism, and regulation. Antioxid Redox Signal. 2014;20(3):460–473. doi: 10.1089/ars.2013.5371
   PubMed Web of Science ®Google Scholar
• Jacomin A-C, Samavedam S, Promponas V, et al. iLIR database: A web resource for LIR motif-containing proteins in eukaryotes. Autophagy. 2016;12(10):1945–1953. doi: 10.1080/15548627.2016.1207016
   PubMed Web of Science ®Google Scholar
• Hale CM, Cheng Q, Ortuno D, et al. Identification of modulators of autophagic flux in an image-based high content siRNA screen. Autophagy. 2016;12(4):713–726. doi: 10.1080/15548627.2016.1147669
   PubMed Web of Science ®Google Scholar
• Guo S, Pridham KJ, Virbasius C-M, et al. A large-scale RNA interference screen identifies genes that regulate autophagy at different stages. Sci Rep. 2018;8(1):2822. doi: 10.1038/s41598-018-21106-5
   PubMedGoogle Scholar
• Szyniarowski P, Corcelle-Termeau E, Farkas T, et al. A comprehensive siRNA screen for kinases that suppress macroautophagy in optimal growth conditions. Autophagy. 2011;7(8):892–903. doi: 10.4161/auto.7.8.15770
   PubMed Web of Science ®Google Scholar
• Bordi M, De Cegli R, Testa B, et al. A gene toolbox for monitoring autophagy transcription. Cell Death Dis. 2021;12(11):1044. doi: 10.1038/s41419-021-04121-9
   PubMed Web of Science ®Google Scholar
• Orvedahl A, Sumpter R, Xiao G, et al. Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature. 2011;480(7375):113–117. doi: 10.1038/nature10546
   PubMed Web of Science ®Google Scholar
• Chan EYW, Kir S, Tooze SA. siRNA screening of the kinome identifies ULK1 as a multidomain modulator of autophagy. J Biol Chem. 2007;282:25464–25474. doi: 10.1074/jbc.M703663200
   PubMed Web of Science ®Google Scholar
• Collier JJ, Guissart C, Oláhová M, et al. Developmental Consequences of Defective ATG7-mediated autophagy in humans. N Engl J Med. 2021;384(25):2406–2417. doi: 10.1056/NEJMoa1915722
   PubMed Web of Science ®Google Scholar
• Ye X, Zhou X-J, Zhang H. Exploring the role of autophagy-related gene 5 (ATG5) Yields important Insights into autophagy in Autoimmune/Autoinflammatory diseases. Front Immunol. 2018;9:2334. doi: 10.3389/fimmu.2018.02334
   PubMed Web of Science ®Google Scholar
• Veres DV, Gyurkó DM, Thaler B, et al. ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. Nucleic Acids Res. 2015;43:D485–93. doi: 10.1093/nar/gku1007
   PubMed Web of Science ®Google Scholar
• Bastian FB, Roux J, Niknejad A, et al. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res. 2021;49(D1):D831–D847. doi: 10.1093/nar/gkaa793
   PubMed Web of Science ®Google Scholar
• Demir E, Cary MP, Paley S, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010;28(9):935–942. doi: 10.1038/nbt.1666
   PubMed Web of Science ®Google Scholar
• Perfetto L, Acencio ML, Bradley G, et al. CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics. 2019;35(19):3779–3785. doi: 10.1093/bioinformatics/btz132
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi: 10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Mao K, Klionsky DJ. Xenophagy: A battlefield between host and microbe, and a possible avenue for cancer treatment. Autophagy. 2017;13:223–224. doi: 10.1080/15548627.2016.1267075
   PubMed Web of Science ®Google Scholar
• Faure M, Lafont F. Pathogen-induced autophagy signaling in innate immunity. J Innate Immun. 2013;5(5):456–470. doi: 10.1159/000350918
   PubMed Web of Science ®Google Scholar
• Wang Z, Li C. Xenophagy in innate immunity: A battle between host and pathogen. Dev Comp Immunol. 2020;109:103693. doi: 10.1016/j.dci.2020.103693
   PubMed Web of Science ®Google Scholar
• Fraser J, Cabodevilla AG, Simpson J, et al. Interplay of autophagy, receptor tyrosine kinase signalling and endocytic trafficking. Essays Biochem. 2017;61:597–607. doi: 10.1042/EBC20170091
   PubMed Web of Science ®Google Scholar
• Deretic V, Saitoh T, Akira S. Autophagy in infection, inflammation and immunity. Nat Rev Immunol. 2013;13(10):722–737. doi: 10.1038/nri3532
   PubMed Web of Science ®Google Scholar
• Burton EA, Plattner R, Pendergast AM. Abl tyrosine kinases are required for infection by Shigella flexneri. EMBO J. 2003;22:5471–5479. doi: 10.1093/emboj/cdg512
   PubMed Web of Science ®Google Scholar
• Napier RJ, Rafi W, Cheruvu M, et al. Imatinib-sensitive tyrosine kinases regulate mycobacterial pathogenesis and represent therapeutic targets against tuberculosis. Cell Host Microbe. 2011;10(5):475–485. doi: 10.1016/j.chom.2011.09.010
   PubMed Web of Science ®Google Scholar
• Yogalingam G, Pendergast AM. Abl kinases regulate autophagy by promoting the trafficking and function of lysosomal components. J Biol Chem. 2008;283(51):35941–35953. doi: 10.1074/jbc.M804543200
   PubMed Web of Science ®Google Scholar
• Wang RC, Wei Y, An Z, et al. Akt-mediated regulation of autophagy and tumorigenesis through beclin 1 phosphorylation. Science. 2012;338(6109):956–959. doi: 10.1126/science.1225967
   PubMed Web of Science ®Google Scholar
• Kaur S, Changotra H. The beclin 1 interactome: Modification and roles in the pathology of autophagy-related disorders. Biochimie. 2020;175:34–49. doi: 10.1016/j.biochi.2020.04.025
   PubMed Web of Science ®Google Scholar
• Shi C-S, Kehrl JH. TRAF6 and A20 regulate lysine 63-linked ubiquitination of beclin-1 to control TLR4-induced autophagy. Sci Signal. 2010;3:ra42. doi: 10.1126/scisignal.2000751
   PubMed Web of Science ®Google Scholar
• Zhao Y, Wang Z, Zhang W, et al. MicroRNAs play an essential role in autophagy regulation in various disease phenotypes. BioFactors. 2019;45(6):844–856. doi: 10.1002/biof.1555
   PubMed Web of Science ®Google Scholar
• Chen Z, Wang T, Liu Z, et al. Inhibition of autophagy by MiR-30A induced by Mycobacteria tuberculosis as a possible mechanism of immune Escape in human Macrophages. Jpn J Infect Dis. 2015;68(5):420–424. doi: 10.7883/yoken.JJID.2014.466
   PubMed Web of Science ®Google Scholar
• Yang X-J, Si R-H, Liang Y-H, et al. Mir-30d increases intracellular survival of Helicobacter pylori through inhibition of autophagy pathway. World J Gastroenterol. 2016;22(15):3978–3991. doi: 10.3748/wjg.v22.i15.3978
   PubMed Web of Science ®Google Scholar
• Mishra R, Krishnamoorthy P, Kumar H. MicroRNA-30e-5p Regulates SOCS1 and SOCS3 during bacterial infection. Front Cell Infect Microbiol. 2020;10:604016. doi: 10.3389/fcimb.2020.604016
   PubMed Web of Science ®Google Scholar
• Zhang F, Zhou Y, Ding J. The current landscape of microRnas (miRnas) in bacterial pneumonia: opportunities and challenges. Cell Mol Biol Lett. 2022;27(1):70. doi: 10.1186/s11658-022-00368-y
   PubMed Web of Science ®Google Scholar
• Fesen K, Silveyra P, Fuentes N, et al. The role of microRnas in chronic pseudomonas lung infection in Cystic fibrosis. Respir med. 2019;151:133–138. doi: 10.1016/j.rmed.2019.04.012
   PubMed Web of Science ®Google Scholar
• Wang S, Xue S, Dai Y, et al. Reduced expression of microRNA-100 confers unfavorable prognosis in patients with bladder cancer. Diagn Pathol. 2012;7(1):159. doi: 10.1186/1746-1596-7-159
   PubMedGoogle Scholar
• Kirisako T, Baba M, Ishihara N, et al. Formation process of autophagosome is traced with Apg8/Aut7p in yeast. J Cell Bio. 1999;147(2):435–446. doi: 10.1083/jcb.147.2.435
   PubMed Web of Science ®Google Scholar
• Chong ZX, Yeap SK, Ho WY. Regulation of autophagy by microRnas in human breast cancer. J Biomed Sci. 2021;28(1):21. doi: 10.1186/s12929-021-00715-9
   PubMed Web of Science ®Google Scholar
• Yan R-L, Luan C-L, Liao C-C, et al. Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival. J Biomed Sci. 2022;29(1):30. doi: 10.1186/s12929-022-00815-0
   PubMed Web of Science ®Google Scholar
• Oughtred R, Stark C, Breitkreutz B-J, et al. The BioGRID interaction database: 2019 update. Nucleic Acids Res. 2019;47(D1):D529–D541. doi: 10.1093/nar/gky1079
   PubMed Web of Science ®Google Scholar
• Teng X, Chen X, Xue H, et al. Npinter v4.0: an integrated database of ncRNA interactions. Nucleic Acids Res. 2020;48:D160–D165. doi: 10.1093/nar/gkz969
   PubMed Web of Science ®Google Scholar
• Liu C-J, Gao C, Ma Z, et al. lncRinter: A database of experimentally validated long non-coding RNA interaction. J Genet Genomics. 2017;44(5):265–268. doi: 10.1016/j.jgg.2017.01.004
   PubMed Web of Science ®Google Scholar
• Nanduri R, Kalra R, Bhagyaraj E, et al. AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy. Autophagy. 2019;15(7):1280–1295. doi: 10.1080/15548627.2019.1571717
   PubMed Web of Science ®Google Scholar
• Yang Y, Klionsky DJ. Autophagy and disease: unanswered questions. Cell Death Differ. 2020;27(3):858–871. doi: 10.1038/s41418-019-0480-9
   PubMed Web of Science ®Google Scholar
• Jiang L-H, Zhang H, Tang J-H. MiR-30a: A novel Biomarker and potential Therapeutic target for cancer. J Oncol. 2018;2018:5167829. doi: 10.1155/2018/5167829
   PubMed Web of Science ®Google Scholar
• Zhu H, Wu H, Liu X, et al. Regulation of autophagy by a beclin 1-targeted microRNA, miR-30a, in cancer cells. Autophagy. 2009;5(6):816–823. doi: 10.4161/auto.9064
   PubMed Web of Science ®Google Scholar
• Chen W, Li Z, Liu H, et al. MicroRNA-30a targets BECLIN-1 to inactivate autophagy and sensitizes gastrointestinal stromal tumor cells to imatinib. Cell Death Dis. 2020;11(3):198. doi: 10.1038/s41419-020-2390-7
   PubMed Web of Science ®Google Scholar
• Xu T, Chu Q, Cui J, et al. MicroRNA-216a inhibits NF-κB-Mediated inflammatory Cytokine Production in teleost fish by modulating p65. Infect Immun. 2018;86(6): doi: 10.1128/IAI.00256-18
   Web of Science ®Google Scholar
• Consortium U, Martin M-J, Orchard S. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021;49:D480–D489. doi: 10.1093/nar/gkaa1100
   PubMed Web of Science ®Google Scholar
• Del Toro N, Shrivastava A, Ragueneau E, et al. The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res. 2022;50(D1):D648–D653. doi: 10.1093/nar/gkab1006
   PubMed Web of Science ®Google Scholar
• Keshava Prasad TS, Goel R, Kandasamy K, et al. Human protein reference database–2009 update. Nucleic Acids Res. 2009;37:D767–72. doi: 10.1093/nar/gkn892
   PubMed Web of Science ®Google Scholar
• Liu W, Li D, Wang J, et al. Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. Mol & Cell Proteomics. 2009;8(9):2063–2070. doi: 10.1074/mcp.M800354-MCP200
   PubMed Web of Science ®Google Scholar
• Rhodes DR, Tomlins SA, Varambally S, et al. Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. 2005;23(8):951–959. doi: 10.1038/nbt1103
   PubMed Web of Science ®Google Scholar
• Vinayagam A, Zirin J, Roesel C, et al. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods. 2014;11(1):94–99. doi: 10.1038/nmeth.2733
   PubMed Web of Science ®Google Scholar
• Ramírez F, Albrecht M. Finding scaffold proteins in interactomes. Trends Cell Biol. 2010;20(1):2–4. doi: 10.1016/j.tcb.2009.11.003
   PubMed Web of Science ®Google Scholar
• Behrends C, Sowa ME, Gygi SP, et al. Network organization of the human autophagy system. Nature. 2010;466(7302):68–76. doi: 10.1038/nature09204
   PubMed Web of Science ®Google Scholar
• Xiao F, Zuo Z, Cai G, et al. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2009;37(Database):D105–10. doi: 10.1093/nar/gkn851
   PubMedGoogle Scholar
• Xu J, Li YH. miRdeathdb: a database bridging microRnas and the programmed cell death. Cell Death Differ. 2012;19:1571. doi: 10.1038/cdd.2012.87
   PubMed Web of Science ®Google Scholar
• Jiang Q, Wang Y, Hao Y, et al. miR2disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009;37(Database):D98–104. doi: 10.1093/nar/gkn714
   PubMedGoogle Scholar
• Wang P, Zhi H, Zhang Y, et al. miRsponge: a manually curated database for experimentally supported miRNA sponges and ceRnas. Database (Oxford). 2015;2015. doi: 10.1093/database/bav098.
   Google Scholar
• Li J-H, Liu S, Zhou H, et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42:D92–7. doi: 10.1093/nar/gkt1248
   PubMed Web of Science ®Google Scholar