ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system

References

• Ambros V. The functions of animal microRNAs. Nature 2004; 431:350-5; PMID:15372042; http://dx.doi.org/10.1038/nature02871
   PubMed Web of Science ®Google Scholar
• DeOcesano-Pereira C, Amaral MS, Parreira KS, Ayupe AC, Jacysyn JF, Amarante-Mendes GP, Reis EM, Verjovski-Almeida S. Long non-coding RNA INXS is a critical mediator of BCL−XS induced apoptosis. Nucleic Acids Res 2014; 42:8343-55; PMID:24992962; http://dx.doi.org/10.1093/nar/gku561
   PubMed Web of Science ®Google Scholar
• Michel CI, Holley CL, Scruggs BS, Sidhu R, Brookheart RT, Listenberger LL, Behlke MA, Ory DS, Schaffer JE. Small nucleolar RNAs U32a, U33, and U35a are critical mediators of metabolic stress. Cell Metab 2011; 14:33-44; PMID:21723502; http://dx.doi.org/10.1016/j.cmet.2011.04.009
   PubMed Web of Science ®Google Scholar
• Sun M, Liu XH, Lu KH, Nie FQ, Xia R, Kong R, Yang JS, Xu TP, Liu YW, Zou YF, et al. EZH2-mediated epigenetic suppression of long noncoding RNA SPRY4-IT1 promotes NSCLC cell proliferation and metastasis by affecting the epithelial-mesenchymal transition. Cell Death Dis 2014; 5:e1298; PMID:24967960; http://dx.doi.org/10.1038/cddis.2014.256
   PubMed Web of Science ®Google Scholar
• Wang Y, Chen L, Chen B, Li X, Kang J, Fan K, Hu Y, Xu J, Yi L, Yang J, et al. Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network. Cell Death Dis 2013; 4:e765; PMID:23928704; http://dx.doi.org/10.1038/cddis.2013.292
   PubMed Web of Science ®Google Scholar
• Gibbings D, Mostowy S, Voinnet O. Autophagy selectively regulates miRNA homeostasis. Autophagy 2013; 9:781-3; PMID:23422216; http://dx.doi.org/10.4161/auto.23694
   PubMed Web of Science ®Google Scholar
• Hwang HW, Mendell JT. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br J Cancer 2007; 96 Suppl:R40-4; PMID:17393584
   PubMed Web of Science ®Google Scholar
• Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 2011; 43:621-9; PMID:21642992; http://dx.doi.org/10.1038/ng.848
   PubMed Web of Science ®Google Scholar
• Eisenberg-Lerner A, Bialik S, Simon HU, Kimchi A. Life and death partners: apoptosis, autophagy and the cross-talk between them. Cell Death Differ 2009; 16:966-75; PMID:19325568; http://dx.doi.org/10.1038/cdd.2009.33
   PubMed Web of Science ®Google Scholar
• Xu J, Wang Y, Tan X, Jing H. MicroRNAs in autophagy and their emerging roles in crosstalk with apoptosis. Autophagy 2012; 8:873-82; PMID:22441107; http://dx.doi.org/10.4161/auto.19629
   PubMed Web of Science ®Google Scholar
• Xu J, Li YH. 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
   PubMed Web of Science ®Google Scholar
• Li Y, Zhuang L, Wang Y, Hu Y, Wu Y, Wang D, Xu J. Connect the dots: a systems level approach for analyzing the miRNA-mediated cell death network. Autophagy 2013; 9:436-9; PMID:23322033; http://dx.doi.org/10.4161/auto.23096
   PubMed Web of Science ®Google Scholar
• Inuzuka H, Shaik S, Onoyama I, Gao D, Tseng A, Maser RS, Zhai B, Wan L, Gutierrez A, Lau AW, et al. SCF(FBW7) regulates cellular apoptosis by targeting MCL1 for ubiquitylation and destruction. Nature 2011; 471:104-9; PMID:21368833; http://dx.doi.org/10.1038/nature09732
   PubMed Web of Science ®Google Scholar
• Day CL, Chen L, Richardson SJ, Harrison PJ, Huang DC, Hinds MG. Solution structure of prosurvival Mcl−1 and characterization of its binding by proapoptotic BH3-only ligands. J Biol Chem 2005; 280:4738-44; PMID:15550399; http://dx.doi.org/10.1074/jbc.M411434200
   PubMed Web of Science ®Google Scholar
• Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, Kim S, Safe S. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene 2013; 32:1616-25; PMID:22614017; http://dx.doi.org/10.1038/onc.2012.193
   PubMed Web of Science ®Google Scholar
• Yang F, Bi J, Xue X, Zheng L, Zhi K, Hua J, Fang G. Up-regulated long non-coding RNA H19 contributes to proliferation of gastric cancer cells. FEBS J 2012; 279:3159-65; PMID:22776265; http://dx.doi.org/10.1111/j.1742-4658.2012.08694.x
   PubMed Web of Science ®Google Scholar
• Zhang A, Zhou N, Huang J, Liu Q, Fukuda K, Ma D, Lu Z, Bai C, Watabe K, Mo YY. The human long non-coding RNA-RoR is a p53 repressor in response to DNA damage. Cell Res 2013; 23:340-50; PMID:23208419; http://dx.doi.org/10.1038/cr.2012.164
   PubMed Web of Science ®Google Scholar
• Zhou Y, Zhang X, Klibanski A. MEG3 noncoding RNA: a tumor suppressor. J Mol Endocrinol 2012; 48:R45-53; PMID:22393162; http://dx.doi.org/10.1530/JME-12-0008
   PubMed Web of Science ®Google Scholar
• Di Martino MT, Leone E, Amodio N, Foresta U, Lionetti M, Pitari MR, Cantafio ME, Gullà A, Conforti F, Morelli E, et al. Synthetic miR-34a mimics as a novel therapeutic agent for multiple myeloma: in vitro and in vivo evidence. Clin Cancer Res 2012; 18:6260-70; PMID:23035210; http://dx.doi.org/10.1158/1078-0432.CCR-12-1708
   PubMed Web of Science ®Google Scholar
• Hu QL, Jiang QY, Jin X, Shen J, Wang K, Li YB, Xu FJ, Tang GP, Li ZH. Cationic microRNA-delivering nanovectors with bifunctional peptides for efficient treatment of PANC-1 xenograft model. Biomaterials 2013; 34:2265-76; PMID:23298779; http://dx.doi.org/10.1016/j.biomaterials.2012.12.016
   PubMed Web of Science ®Google Scholar
• Rucker FG, Russ AC, Cocciardi S, Kett H, Schlenk RF, Botzenhardt U, Langer C, Krauter J, Fröhling S, Schlegelberger B, et al. Altered miRNA and gene expression in acute myeloid leukemia with complex karyotype identify networks of prognostic relevance. Leukemia 2013; 27:353-61; PMID:22810507; http://dx.doi.org/10.1038/leu.2012.208
   PubMed Web of Science ®Google Scholar
• Frankel LB, Lund AH. MicroRNA regulation of autophagy. Carcinogenesis 2012; 33:2018-25; PMID:22902544; http://dx.doi.org/10.1093/carcin/bgs266
   PubMed Web of Science ®Google Scholar
• Cosentino Lagomarsino M, Jona P, Bassetti B, Isambert H. Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci U S A 2007; 104:5516-20; PMID:17372223; http://dx.doi.org/10.1073/pnas.0609023104
   PubMed Web of Science ®Google Scholar
• Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, 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
   PubMed Web of Science ®Google Scholar
• Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 2006; 103:14724-31; PMID:17003135; http://dx.doi.org/10.1073/pnas.0508637103
   PubMed Web of Science ®Google Scholar
• Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, et al. Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol 2011; 7:e1002190; PMID:22125477; http://dx.doi.org/10.1371/journal.pcbi.1002190
   PubMed Web of Science ®Google Scholar
• Ravasz E, Barabasi AL. Hierarchical organization in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys 2003; 67:026112; PMID:12636753; http://dx.doi.org/10.1103/PhysRevE.67.026112
   PubMed Web of Science ®Google Scholar
• Wuchty S, Almaas E. Peeling the yeast protein network. Proteomics 2005; 5:444-9; PMID:15627958; http://dx.doi.org/10.1002/pmic.200400962
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes–2009. Nucleic Acids Res 2010; 38:D497-501; PMID:19884131; http://dx.doi.org/10.1093/nar/gkp914
   PubMed Web of Science ®Google Scholar
• Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116:281-97; PMID:14744438; http://dx.doi.org/10.1016/S0092-8674(04)00045-5
   PubMed Web of Science ®Google Scholar
• Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 2007; 8:209-20; PMID:17318225; http://dx.doi.org/10.1038/nrm2124
   PubMed Web of Science ®Google Scholar
• Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10:155-9; PMID:19188922; http://dx.doi.org/10.1038/nrg2521
   PubMed Web of Science ®Google Scholar
• Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43:904-14; PMID:21925379; http://dx.doi.org/10.1016/j.molcel.2011.08.018
   PubMed Web of Science ®Google Scholar
• Kang R, Zeh HJ, Lotze MT, Tang D. The Beclin 1 network regulates autophagy and apoptosis. Cell Death Differ 2011; 18:571-80; PMID:21311563; http://dx.doi.org/10.1038/cdd.2010.191
   PubMed Web of Science ®Google Scholar
• Galluzzi L, Vitale I, Abrams JM, Alnemri ES, Baehrecke EH, Blagosklonny MV, Dawson TM, Dawson VL, El-Deiry WS, Fulda S, et al. Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death Differ 2012; 19:107-20; PMID:21760595; http://dx.doi.org/10.1038/cdd.2011.96
   PubMed Web of Science ®Google Scholar
• Marino G, Niso-Santano M, Baehrecke EH, Kroemer G. Self-consumption: the interplay of autophagy and apoptosis. Nat Rev Mol Cell Biol 2014; 15:81-94; PMID:24401948; http://dx.doi.org/10.1038/nrm3735
   PubMed Web of Science ®Google Scholar
• Vanden Berghe T, Linkermann A, Jouan-Lanhouet S, Walczak H, Vandenabeele P. Regulated necrosis: the expanding network of non-apoptotic cell death pathways. Nat Rev Mol Cell Biol 2014; 15:135-47; PMID:24452471; http://dx.doi.org/10.1038/nrm3737
   PubMed Web of Science ®Google Scholar
• Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 2015; 43:D168-73; PMID:25332394; http://dx.doi.org/10.1093/nar/gku988
   PubMed Web of Science ®Google Scholar
• Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. Ensembl 2014. Nucleic Acids Res 2014; 42:D749-55; PMID:24316576; http://dx.doi.org/10.1093/nar/gkt1196
   PubMed Web of Science ®Google Scholar
• Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 2014; 42:D68-73; PMID:24275495; http://dx.doi.org/10.1093/nar/gkt1181
   PubMed Web of Science ®Google Scholar
• Xie J, Zhang M, Zhou T, Hua X, Tang L, Wu W. Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. Nucleic Acids Res 2007; 35:D183-7; PMID:17099227; http://dx.doi.org/10.1093/nar/gkl873
   PubMed Web of Science ®Google Scholar
• Lestrade L, Weber MJ. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 2006; 34:D158-62; PMID:16381836; http://dx.doi.org/10.1093/nar/gkj002
   PubMed Web of Science ®Google Scholar
• John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004; 2:e363; PMID:15502875; http://dx.doi.org/10.1371/journal.pbio.0020363
   PubMed Web of Science ®Google Scholar
• Wenzel A, Akbasli E, Gorodkin J. RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Bioinformatics 2012; 28:2738-46; PMID:22923300; http://dx.doi.org/10.1093/bioinformatics/bts519
   PubMed Web of Science ®Google Scholar
• Wang L, Huang C, Yang MQ, Yang JY. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol 2010; 4 Suppl 1:S3; PMID:20522253; http://dx.doi.org/10.1186/1752-0509-4-S1-S3
   PubMedGoogle Scholar
• Terribilini M, Sander JD, Lee JH, Zaback P, Jernigan RL, Honavar V, Dobbs D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res 2007; 35:W578-84; PMID:17483510; http://dx.doi.org/10.1093/nar/gkm294
   PubMed Web of Science ®Google Scholar
• Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003; 115:787-98; PMID:14697198; http://dx.doi.org/10.1016/S0092-8674(03)01018-3
   PubMed Web of Science ®Google Scholar
• Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2015; 43:D6-17; PMID:25398906; http://dx.doi.org/10.1093/nar/gku1130
   PubMed Web of Science ®Google Scholar
• Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 2005; 1:e13; PMID:16103902; http://dx.doi.org/10.1371/journal.pcbi.0010013
   PubMed Web of Science ®Google Scholar
• Lin CC, Mitra R, Zhao Z. A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. PloS One 2014; 9:e103142; PMID:25054916; http://dx.doi.org/10.1371/journal.pone.0103142
   PubMed Web of Science ®Google Scholar
• 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:D767-72; PMID:18988627; http://dx.doi.org/10.1093/nar/gkn892
   PubMed Web of Science ®Google Scholar
• Zhang X, Wu D, Chen L, Li X, Yang J, Fan D, Dong T, Liu M, Tan P, Xu J, et al. RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. RNA 2014; 20:989-93; PMID:24803509; http://dx.doi.org/10.1261/rna.044776.114
   PubMed Web of Science ®Google Scholar
• Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, 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
   PubMed Web of Science ®Google Scholar
• Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics 2008; 24:282-4; PMID:18006545; http://dx.doi.org/10.1093/bioinformatics/btm554
   PubMed Web of Science ®Google Scholar
• Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Computat Biol 2007; 3:e59; PMID:17447836; http://dx.doi.org/10.1371/journal.pcbi.0030059
   PubMed Web of Science ®Google Scholar
• Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res 2004; 14:1310-4; PMID:15231746; http://dx.doi.org/10.1101/gr.2300204
   PubMed Web of Science ®Google Scholar
• Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods 2012; 9:471-2; PMID:22426491; http://dx.doi.org/10.1038/nmeth.1938
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13:2498-504; PMID:14597658; http://dx.doi.org/10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Ulitsky I, Shamir R. Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol 2007; 3:104; PMID:17437029; http://dx.doi.org/10.1038/msb4100144
   PubMed Web of Science ®Google Scholar