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Research Paper

AURA 2

Empowering discovery of post-transcriptional networks

, , , , , & show all
Article: e27738 | Received 04 Nov 2013, Accepted 05 Jan 2014, Published online: 29 Jan 2014

References

  • Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. Global quantification of mammalian gene expression control. Nature 2011; 473:337 - 42; http://dx.doi.org/10.1038/nature10098; PMID: 21593866
  • Vogel C, Abreu RdeS, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol 2010; 6:400; http://dx.doi.org/10.1038/msb.2010.59; PMID: 20739923
  • Tebaldi T, Re A, Viero G, Pegoretti I, Passerini A, Blanzieri E, Quattrone A. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. BMC Genomics 2012; 13:220; http://dx.doi.org/10.1186/1471-2164-13-220; PMID: 22672192
  • Melamed D, Eliyahu E, Arava Y. Exploring translation regulation by global analysis of ribosomal association. Methods 2009; 48:301 - 5; http://dx.doi.org/10.1016/j.ymeth.2009.04.020; PMID: 19426805
  • Ingolia NT. Genome-wide translational profiling by ribosome footprinting. Methods Enzymol 2010; 470:119 - 42; http://dx.doi.org/10.1016/S0076-6879(10)70006-9; PMID: 20946809
  • Keene JD, Komisarow JM, Friedersdorf MB. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 2006; 1:302 - 7; http://dx.doi.org/10.1038/nprot.2006.47; PMID: 17406249
  • Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003; 302:1212 - 5; http://dx.doi.org/10.1126/science.1090095; PMID: 14615540
  • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr., Jungkamp AC, Munschauer M, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010; 141:129 - 41; http://dx.doi.org/10.1016/j.cell.2010.03.009; PMID: 20371350
  • König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 2010; 17:909 - 15; http://dx.doi.org/10.1038/nsmb.1838; PMID: 20601959
  • Dassi E, Quattrone A. Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression. RNA Biol 2012; 9:1224 - 32; http://dx.doi.org/10.4161/rna.22035; PMID: 22995832
  • Barreau C, Paillard L, Osborne HB. AU-rich elements and associated factors: are there unifying principles?. Nucleic Acids Res 2005; 33:7138 - 50; http://dx.doi.org/10.1093/nar/gki1012; PMID: 16391004
  • Pan T. N6-methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem Sci 2013; 38:204 - 9; http://dx.doi.org/10.1016/j.tibs.2012.12.006; PMID: 23337769
  • Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 2012; 40:5023 - 33; http://dx.doi.org/10.1093/nar/gks144; PMID: 22344696
  • Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, Chen R, Rohl CA, Johnson JM, Babak T. A quantitative atlas of polyadenylation in five mammals. Genome Res 2012; 22:1173 - 83; http://dx.doi.org/10.1101/gr.132563.111; PMID: 22454233
  • Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 2013; 41:D1 D64 - 9; http://dx.doi.org/10.1093/nar/gks1048; PMID: 23155063
  • Friedel CC, Dölken L, Ruzsics Z, Koszinowski UH, Zimmer R. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res 2009; 37:e115; http://dx.doi.org/10.1093/nar/gkp542; PMID: 19561200
  • Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res 2012; 22:947 - 56; http://dx.doi.org/10.1101/gr.130559.111; PMID: 22369889
  • Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL. AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res 2011; 39:D1 D66 - 9; http://dx.doi.org/10.1093/nar/gkq990; PMID: 21071424
  • UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 2013; 41:D1 D43 - 7; http://dx.doi.org/10.1093/nar/gks1068; PMID: 23161681
  • Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 2011; 39:D1 D301 - 8; http://dx.doi.org/10.1093/nar/gkq1069; PMID: 21036867
  • Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 2013; 499:172 - 7; http://dx.doi.org/10.1038/nature12311; PMID: 23846655
  • Helwak A, Kudla G, Dudnakova T, Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 2013; 153:654 - 65; http://dx.doi.org/10.1016/j.cell.2013.03.043; PMID: 23622248
  • Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, et al. Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res 2012; 22:2208 - 18; http://dx.doi.org/10.1101/gr.139568.112; PMID: 22879431
  • Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci U S A 2012; 109:E2424 - 32; http://dx.doi.org/10.1073/pnas.1207846109; PMID: 22927429
  • Yamashita R, Suzuki Y, Takeuchi N, Wakaguri H, Ueda T, Sugano S, Nakai K. Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res 2008; 36:3707 - 15; http://dx.doi.org/10.1093/nar/gkn248; PMID: 18480124
  • Dassi E, Zuccotti P, Leo S, Provenzani A, Assfalg M, D’Onofrio M, Riva P, Quattrone A. Hyper conserved elements in vertebrate mRNA 3′-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. Nucleic Acids Res 2013; 41:3201 - 16; http://dx.doi.org/10.1093/nar/gkt017; PMID: 23376935
  • Kiran A, Baranov PV. DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 2010; 26:1772 - 6; http://dx.doi.org/10.1093/bioinformatics/btq285; PMID: 20547637
  • Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29:308 - 11; http://dx.doi.org/10.1093/nar/29.1.308; PMID: 11125122
  • 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 2011; 39:D1 D945 - 50; http://dx.doi.org/10.1093/nar/gkq929; PMID: 20952405
  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421; http://dx.doi.org/10.1186/1471-2105-10-421; PMID: 20003500
  • Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res 2009; 19:1630 - 8; http://dx.doi.org/10.1101/gr.094607.109; PMID: 19570905
  • GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet 2013; 45:580 - 5; http://dx.doi.org/10.1038/ng.2653; PMID: 23715323
  • Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25:1974 - 5; http://dx.doi.org/10.1093/bioinformatics/btp250; PMID: 19398448
  • Kasprzyk A. BioMart: driving a paradigm change in biological data management. Database 2011,2011:bar049.
  • Chang SH, Hla T. Gene regulation by RNA binding proteins and microRNAs in angiogenesis. Trends Mol Med 2011; 17:650 - 8; http://dx.doi.org/10.1016/j.molmed.2011.06.008; PMID: 21802991
  • Sharma S, Verma S, Vasudevan M, Samanta S, Thakur JK, Kulshreshtha R. The interplay of HuR and miR-3134 in regulation of AU rich transcriptome. RNA Biol 2013; 10:1283 - 90; http://dx.doi.org/10.4161/rna.25482; PMID: 23823647
  • Yoon JH, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S, Huarte M, Zhan M, Becker KG, Gorospe M. LincRNA-p21 suppresses target mRNA translation. Mol Cell 2012; 47:648 - 55; http://dx.doi.org/10.1016/j.molcel.2012.06.027; PMID: 22841487
  • Python. (http://www.python.org/)
  • Django. (http://www.djangoproject.com/)
  • JQuery User Interface. . http://jqueryui.com/
  • Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an interactive web-based network browser. Bioinformatics 2010; 26:2347 - 8; http://dx.doi.org/10.1093/bioinformatics/btq430; PMID: 20656902
  • HUGO Gene Nomenclature Committee at the European Bioinformatics Institute. . http://www.genenames.org
  • Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE, Mouse Genome Database Group. The mouse genome database: genotypes, phenotypes, and models of human disease. Nucleic Acids Res 2013; 41:D1 D885 - 91; http://dx.doi.org/10.1093/nar/gks1115; PMID: 23175610
  • Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, et al. Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 2010; 28:1248 - 50; http://dx.doi.org/10.1038/nbt1210-1248; PMID: 21139605
  • Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011; 39:D1 D152 - 7; http://dx.doi.org/10.1093/nar/gkq1027; PMID: 21037258
  • 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:D1 D54 - 60; http://dx.doi.org/10.1093/nar/gkn783; PMID: 18971253
  • The Gene Ontology. . http://amigo.geneontology.org
  • Vanderkraats ND, Hiken JF, Decker KF, Edwards JR. Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes. Nucleic Acids Res 2013; 41:6816 - 27; http://dx.doi.org/10.1093/nar/gkt482; PMID: 23748561
  • Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M. A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods 2011; 8:559 - 64; http://dx.doi.org/10.1038/nmeth.1608; PMID: 21572407
  • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25:1915 - 27; http://dx.doi.org/10.1101/gad.17446611; PMID: 21890647
  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511 - 5; http://dx.doi.org/10.1038/nbt.1621; PMID: 20436464