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Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy

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Pages 155-165 | Received 18 May 2014, Accepted 15 Oct 2014, Published online: 30 Jan 2015

References

  • Hamacher-Brady A. Autophagy regulation and integration with cell signaling. Antioxid Redox Signal 2012; 17:756-65; PMID:22149388; http://dx.doi.org/10.1089/ars.2011.4410
  • Frankel LB, Lund AH. MicroRNA regulation of autophagy. Carcinogenesis 2012; 33:2018-25; PMID:22902544; http://dx.doi.org/10.1093/carcin/bgs266
  • Boya P, Reggiori F, Codogno P. Emerging regulation and functions of autophagy. Nat Cell Biol 2013; 15:713-20; PMID:23817233; http://dx.doi.org/10.1038/ncb2788
  • Wen S, Niu Y, Lee SO, Chang C. Androgen receptor (AR) positive vs negative roles in prostate cancer cell deaths including apoptosis, anoikis, entosis, necrosis and autophagic cell death. Cancer Treat Rev 2014; 40:31-40; PMID:23993415; http://dx.doi.org/10.1016/j.ctrv.2013.07.008
  • Reggiori F. Autophagy: New questions from recent answers. ISRN Mol Biol 2012; 2012:1-12; http://dx.doi.org/10.5402/2012/738718
  • Russell RC, Tian Y, Yuan H, Park HW, Chang Y-Y, Kim J, Kim H, Neufeld TP, Dillin A, Guan K-L. ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol 2013; 15:741-50; PMID:23685627; http://dx.doi.org/10.1038/ncb2757
  • Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes CA, Maiolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, et al. Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Mol Cell 2014; 53:471-83; PMID:24440502; http://dx.doi.org/10.1016/j.molcel.2013.12.011
  • Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, et al. TFEB links autophagy to lysosomal biogenesis. Science 2011; 332:1429-33; PMID:21617040; http://dx.doi.org/10.1126/science.1204592
  • Salih DAM, Brunet A. FoxO transcription factors in the maintenance of cellular homeostasis during aging. Curr Opin Cell Biol 2008; 20:126-36; PMID:18394876; http://dx.doi.org/10.1016/j.ceb.2008.02.005
  • Seo Y-K, Jeon T-I, Chong HK, Biesinger J, Xie X, Osborne TF. Genome-wide localization of SREBP-2 in hepatic chromatin predicts a role in autophagy. Cell Metab 2011; 13:367-75; PMID:21459322; http://dx.doi.org/10.1016/j.cmet.2011.03.005
  • Lavallard VJ, Meijer AJ, Codogno P, Gual P. Autophagy, signaling and obesity. Pharmacol Res 2012; 66:513-25; PMID:22982482; http://dx.doi.org/10.1016/j.phrs.2012.09.003
  • Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008; 133:1106-17; PMID:18555785; http://dx.doi.org/10.1016/j.cell.2008.04.043
  • Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al. Diversity and complexity in DNA recognition by transcription factors. Science 2009; 324:1720-3; PMID:19443739; http://dx.doi.org/10.1126/science.1162327
  • Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, et al. DNA-binding specificities of human transcription factors. Cell 2013; 152:327-39; PMID:23332764; http://dx.doi.org/10.1016/j.cell.2012.12.009
  • Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 2010; 38:D105-110; PMID:19906716; http://dx.doi.org/10.1093/nar/gkp950
  • Chen N, Karantza V. Autophagy as a therapeutic target in cancer. Cancer Biol Ther 2011; 11:157-68; PMID:21228626; http://dx.doi.org/10.4161/cbt.11.2.14622
  • Kubisch J, Türei D, Földvári-Nagy L, Dunai ZA, Zsákai L, Varga M, Vellai T, Csermely P, Korcsmáros T. Complex regulation of autophagy in cancer - integrated approaches to discover the networks that hold a double-edged sword. Semin Cancer Biol 2013; 23:252-61; PMID:23810837; http://dx.doi.org/10.1016/j.semcancer.2013.06.009
  • Santra T, Kolch W, Kholodenko BN. Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PLoS Comput Biol 2014; 10:e1003385; PMID:24550716; http://dx.doi.org/10.1371/journal.pcbi.1003385
  • Moussay E, Kaoma T, Baginska J, Muller A, Van Moer K, Nicot N, Nazarov PV, Vallar L, Chouaib S, Berchem G, et al. The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray. Autophagy 2011; 7:760-70; PMID:21490427; http://dx.doi.org/10.4161/auto.7.7.15454
  • 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:D986-990; PMID:20972215; http://dx.doi.org/10.1093/nar/gkq995
  • Behrends C, Sowa ME, Gygi SP, Harper JW. Network organization of the human autophagy system. Nature 2010; 466:68-76; PMID:20562859; http://dx.doi.org/10.1038/nature09204
  • Lista P, Straface E, Brunelleschi S, Franconi F, Malorni W. On the role of autophagy in human diseases: a gender perspective. J Cell Mol Med 2011; 15:1443-57; PMID:21362130; http://dx.doi.org/10.1111/j.1582-4934.2011.01293.x
  • Bhupathy P, Haines CD, Leinwand LA. Influence of sex hormones and phytoestrogens on heart disease in men and women. Womens Health 2010; 6:77-95.
  • Bouma W, Noma M, Kanemoto S, Matsubara M, Leshnower BG, Hinmon R, Gorman JH, Gorman RC. Sex-related resistance to myocardial ischemia-reperfusion injury is associated with high constitutive ARC expression. AJP Heart Circ Physiol 2010; 298:H1510-H1517; http://dx.doi.org/10.1152/ajpheart.01021.2009
  • Chen C, Hu L-X, Dong T, Wang G-Q, Wang L-H, Zhou X-P, Jiang Y, Murao K, Lu S-Q, Chen J-W, et al. Apoptosis and autophagy contribute to gender difference in cardiac ischemia-reperfusion induced injury in rats. Life Sci 2013; 93:265-70; PMID:23827240; http://dx.doi.org/10.1016/j.lfs.2013.06.019
  • Weis SN, Toniazzo AP, Ander BP, Zhan X, Careaga M, Ashwood P, Wyse ATS, Netto CA, Sharp FR. Autophagy in the brain of neonates following hypoxia-ischemia shows sex- and region-specific effects. Neuroscience 2014; 256:201-9; PMID:24184979; http://dx.doi.org/10.1016/j.neuroscience.2013.10.046
  • Zhu C, Xu F, Wang X, Shibata M, Uchiyama Y, Blomgren K, Hagberg H. Different apoptotic mechanisms are activated in male and female brains after neonatal hypoxia-ischaemia. J Neurochem 2006; 96:1016-27; PMID:16412092; http://dx.doi.org/10.1111/j.1471-4159.2005.03639.x
  • Barbati C, Pierdominici M, Gambardella L, Malchiodi Albedi F, Karas RH, Rosano G, Malorni W, Ortona E. Cell surface estrogen receptor alpha is upregulated during subchronic metabolic stress and inhibits neuronal cell degeneration. PLoS ONE 2012; 7:e42339; PMID:22860116; http://dx.doi.org/10.1371/journal.pone.0042339
  • Bovolenta LA, Acencio ML, Lemke N. HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. BMC Genomics 2012; 13:405; PMID:22900683; http://dx.doi.org/10.1186/1471-2164-13-405
  • Proikas-Cezanne T, Waddell S, Gaugel A, Frickey T, Lupas A, Nordheim A. WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene 2004; 23:9314-25; PMID:15602573; http://dx.doi.org/10.1038/sj.onc.1208331
  • Alvarez MA, Yan C. A graph-based semantic similarity measure for the gene ontology. J Bioinform Comput Biol 2011; 9:681-95; PMID:22084008; http://dx.doi.org/10.1142/S0219720011005641
  • Kremling A, Saez-Rodriguez J. Systems biology - An engineering perspective. J Biotechnol 2007; 129:329-51; PMID:17400319; http://dx.doi.org/10.1016/j.jbiotec.2007.02.009
  • Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA. Logic-based models for the analysis of cell signaling networks. Biochemistry (Mosc) 2010; 49:3216-24; http://dx.doi.org/10.1021/bi902202q
  • Maus C, Rybacki S, Uhrmacher AM. Rule-based multi-level modeling of cell biological systems. BMC Syst Biol 2011; 5:166; PMID:22005019; http://dx.doi.org/10.1186/1752-0509-5-166
  • Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: A novel paradigm of drug discovery. Pharmacol Ther 2013; 138:333-408; PMID:23384594; http://dx.doi.org/10.1016/j.pharmthera.2013.01.016
  • Chen H, Sharp BM. Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 2004; 5:147; PMID:15473905; http://dx.doi.org/10.1186/1471-2105-5-147
  • Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004; 36:664; PMID:15226743; http://dx.doi.org/10.1038/ng0704-664
  • Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M. A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics 2009; 10:351; PMID:19852836; http://dx.doi.org/10.1186/1471-2105-10-351
  • Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res 2011; 40:D290-D301; PMID:22127870; http://dx.doi.org/10.1093/nar/gkr1065
  • Blanco E, Farré D, Albà MM, Messeguer X, Guigó R. ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Res 2006; 34:D63-67; PMID:16381947; http://dx.doi.org/10.1093/nar/gkj116
  • Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, et al. Architecture of the human regulatory network derived from ENCODE data. Nature 2012; 489:91-100; PMID:22955619; http://dx.doi.org/10.1038/nature11245
  • Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 2008; 36:D107-113; PMID:18006570; http://dx.doi.org/10.1093/nar/gkm967
  • Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res 2009; 37:D54-60; PMID:18971253; http://dx.doi.org/10.1093/nar/gkn783
  • Chatr-aryamontri A, Breitkreutz B-J, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O’Donnell L, et al. The BioGRID interaction database: 2013 update. Nucleic Acids Res 2012; 41:D816-D823; PMID:23203989; http://dx.doi.org/10.1093/nar/gks1158
  • Breuer K, Foroushani AK, Laird MR, Chen C, Sribnaia A, Lo R, Winsor GL, Hancock REW, Brinkman FSL, Lynn DJ. InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Res 2012; 41:D1228-D1233; PMID:23180781; http://dx.doi.org/10.1093/nar/gks1147
  • Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, et al. The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 2013; 42:D358-D363; PMID:24234451; http://dx.doi.org/10.1093/nar/gkt1115
  • Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 2009; 37:D767-772; PMID:18988627; http://dx.doi.org/10.1093/nar/gkn892
  • Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2009; 37:D98-104; PMID:18927107; http://dx.doi.org/10.1093/nar/gkn714
  • Xu J, Li Y-H. miRDeathDB: a database bridging microRNAs and the programmed cell death. Cell Death Differ 2012; 19:1571; PMID:22743998; http://dx.doi.org/10.1038/cdd.2012.87
  • Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009; 37:D105-110; PMID:18996891; http://dx.doi.org/10.1093/nar/gkn851
  • Hsu S-D, Tseng Y-T, Shrestha S, Lin Y-L, Khaleel A, Chou C-H, Chu C-F, Huang H-Y, Lin C-M, Ho S-Y, et al. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res 2014; 42:D78-85; PMID:24304892; http://dx.doi.org/10.1093/nar/gkt1266
  • Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 2012; 40:D222-229; PMID:22135297; http://dx.doi.org/10.1093/nar/gkr1161
  • Bandyopadhyay S, Bhattacharyya M. PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics 2010; 11:190; PMID:20398296; http://dx.doi.org/10.1186/1471-2105-11-190
  • Wang J, Lu M, Qiu C, Cui Q. TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res 2010; 38:D119-122; PMID:19786497; http://dx.doi.org/10.1093/nar/gkp803
  • Fazekas D, Koltai M, Türei D, Módos D, Pálfy M, Dúl Z, Zsákai L, Szalay-Bekő M, Lenti K, Farkas IJ, et al. SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol 2013; 7:7; PMID:23331499; http://dx.doi.org/10.1186/1752-0509-7-7
  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-9; PMID:10802651; http://dx.doi.org/10.1038/75556
  • Becker KG, Barnes KC, Bright TJ, Wang SA. The genetic association database. Nat Genet 2004; 36:431-2; PMID:15118671; http://dx.doi.org/10.1038/ng0504-431
  • McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD). Online Mendelian Inheritance in Man, OMIM. ; Internet. 2014 ; cited 2014 Aug 1; Available from: http://www.ncbi.nlm.nih.gov/omim
  • Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al. COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res 2010; 39:D945-D950; PMID:20952405; http://dx.doi.org/10.1093/nar/gkq929
  • Raghavachari B, Tasneem A, Przytycka TM, Jothi R. DOMINE: a database of protein domain interactions. Nucleic Acids Res 2007; 36:D656-D661; PMID:17913741; http://dx.doi.org/10.1093/nar/gkm761
  • Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Rattei T, Frishman D, et al. The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res 2009; 38:D540-D544; PMID:19920129; http://dx.doi.org/10.1093/nar/gkp1026