Guidelines for the functional annotation of microRNAs using the Gene Ontology

RNA

Volumn 22, Issue 5, 2016, Pages 667-676

  Huntley, Rachael P ^a   Sitnikov, Dmitry ^b   Orlic Milacic, Marija ^c   Balakrishnan, Rama ^d   D'Eustachio, Peter ^e   Gillespie, Marc E ^f   Howe, Doug ^g   Kalea, Anastasia Z ^a   Maegdefessel, Lars ^h   Osumi Sutherland, David ⁱ   Petri, Victoria ^j   Smith, Jennifer R ^j   Van Auken, Kimberly ^k   Wood, Valerie ^l   Zampetaki, Anna ^m   Mayr, Manuel ^m   Lovering, Ruth C ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b JACKSON LABORATORY   (United States)

^c ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^d STANFORD UNIVERSITY   (United States)

^e NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f ST JOHN'S UNIVERSITY   (United States)

^g UNIVERSITY OF OREGON   (United States)

^h KAROLINSKA INSTITUTE   (Sweden)

ⁱ WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^j MEDICAL COLLEGE OF WISCONSIN   (United States)

^k CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^l UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^m KING'S COLLEGE LONDON   (United Kingdom)

more..

Author keywords

Analysis; Annotation; Biocuration; Function; GO; MicroRNA

Indexed keywords

ADENYLATE CYCLASE; MESSENGER RNA; MICRORNA; PROTEIN;

ARTICLE; BIOGENESIS; CONTROLLED STUDY; ENZYME ACTIVITY; GENE FUNCTION; GENE ONTOLOGY; GENE SILENCING; HUMAN; MOLECULAR BIOLOGY; MOLECULAR GENETICS; NONHUMAN; ONTOLOGY DEVELOPMENT; PRACTICE GUIDELINE; PRIORITY JOURNAL; ANIMAL; GENETICS; MOUSE;

ANIMALS; GENE SILENCING; GUIDELINES AS TOPIC; HUMANS; MICE; MICRORNAS;

EID: 84964414557     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.055301.115     Document Type: Article

References (41)

1. Afonso-Grunz F, Müller S. 2015. Principles of miRNA-mRNA interactions: beyond sequence complementarity. Cell Mol Life Sci 72: 3127-3141.
2. Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, et al. 2011. The impact of focused gene ontology curation of specific mammalian systems. PLoS One 6: e27541.
3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
4. Axtell MJ, Westholm JO, Lai EC. 2011. Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biol 12: 221.
5. Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM. 2013. A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) 2013: bat054.
6. Betel D, Wilson M, Gabow A, Marks DS, Sander C. 2008. The microRNA. org resource: targets and expression. Nucleic Acids Res 36: D149-D153.
7. Betel D, Koppal A, Agius P, Sander C, Leslie C. 2010. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11: R90.
8. Bleazard T, Lamb JA, Griffiths-Jones S. 2015. Bias in microRNA functional enrichment analysis. Bioinformatics 31: 1592-1598.
9. Caputo M, Saif J, Rajakaruna C, Brooks M, Angelini GD, Emanueli C. 2015. MicroRNAs in vascular tissue engineering and post-ischemic neovascularization. Adv Drug Deliv Rev 88: 78-91.
10. Castaldi A, Zaglia T, Di Mauro V, Carullo P, Viggiani G, Borile G, Di Stefano B, Schiattarella GG, Gualazzi MG, Elia L. 2014. MicroRNA-133 modulates the β1-adrenergic receptor transduction cascade. Circ Res 115: 273-283.
11. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ. 2006. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38: 228-233.
12. Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, Yang CD, Hong HC, Wei TY, Tu SJ, et al. 2015. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res 44: D239-D247.
13. Clément T, Salone V, Rederstorff M. 2015. Dual luciferase gene reporter assays to study miRNA function. Methods Mol Biol 1296: 187-198.
14. Dangwal S, Bang C, Thum T. 2012. Novel techniques and targets in cardiovascular microRNA research. Cardiovasc Res 93: 545-554.
15. Ekimler S, Sahin K. 2014. Computational methods for microRNA target prediction. Genes 5: 671-683.
16. Emanueli C, Shearn AIU, Angelini GD, Sahoo S. 2015. Exosomes and exosomal miRNAs in cardiovascular protection and repair. Vascul Pharmacol 71: 24-30.
17. Filipowicz W, Bhattacharyya SN, Sonenberg N. 2008. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9: 102-114.
18. The Gene Ontology Consortium. 2014. Gene Ontology Consortium: going forward. Nucleic Acids Res 43: D1049-D1056.
19. Grimson A, Farh KK-H, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
20. Hausser J, Syed AP, Bilen B, Zavolan M. 2013. Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res 23: 604-615.
21. Huang DW, Sherman BT, Lempicki RA. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
22. Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, et al. 2014. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics 15: 155.
23. Janssen HLA, Reesink HW, Lawitz EJ, Zeuzem S, Rodriguez-Torres M, Patel K, van der Meer AJ, Patick AK, Chen A, Zhou Y, et al. 2013. Treatment of HCV infection by targeting microRNA. N Engl J Med 368: 1685-1694.
24. Kalea AZ, Hoteit R, Suvan J, Lovering RC, Palmen J, Cooper JA, Khodiyar VK, Harrington Z, Humphries SE, D'Aiuto F. 2015. Upregulation of gingival tissue miR-200b in obese periodontitis subjects. J Dent Res 94: 59S-69S.
25. Khatri P, Sirota M, Butte A. 2012. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 8: e1002375.
26. Kozomara A, Griffiths-Jones S. 2014. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42: D68-D73.
27. Liu G, Ding M, Chen J, Huang J, Wang H, Jing Q, Shen B. 2010. Computational analysis of microRNA function in heart development. Acta Biochim Biophys Sin (Shanghai) 42: 662-670.
28. Maegdefessel L, Azuma J, Toh R, Merk DR, Deng A, Chin JT, Raaz U, Schoelmerich AM, Raiesdana A, Leeper NJ, et al. 2012. Inhibition of microRNA-29b reduces murine abdominal aortic aneurysm development. J Clin Invest 122: 497-506.
29. Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R. 2013. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford) 2013: bas062.
30. The RNAcentral Consortium. 2015. RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res 43: D123-D129.
31. Soh J, Iqbal J, Queiroz J, Fernandez-Hernando C, Hussain MM. 2013. MicroRNA-30c reduces hyperlipidemia and atherosclerosis in mice by decreasing lipid synthesis and lipoprotein secretion. Nat Med 19: 892-900.
32. Thomson DW, Bracken CP, Goodall GJ. 2011. Experimental strategies for microRNA target identification. Nucleic Acids Res 39: 6845-6853.
33. van Rooij E, Marshall WS, Olson EN. 2008. Toward microRNA-based therapeutics for heart disease: the sense in antisense. Circ Res 103: 919-928.
34. Wakiyama M, Takimoto K, Ohara O, Yokoyama S. 2007. Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev 21: 1857-1862.
35. Wang X, El Naqa IM 2008. Prediction of both conserved and noncon-served microRNA targets in animals. Bioinformatics 24: 325-332.
36. Wang JJ, Guo HS. 2015. Cleavage of INDOLE-3-ACETIC ACID INDUCIBLE28 mRNA by microRNA847 upregulates auxin signaling to modulate cell proliferation and lateral organ growth in Arabidopsis. Plant Cell 27: 574-590.
37. Wilczynska A, Bushell M. 2014. The complexity of miRNA-mediated repression. Cell Death Differ 22: 22-33.
38. Xie M, Zhang S, Yu B. 2015. microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 72: 87-99.
39. Zampetaki A, Attia R, Mayr U, Gomes RSM, Phinikaridou A, Yin X, Langley SR, Willeit P, Lu R, Fanshawe B, et al. 2014. Role of miR-195 in aortic aneurysmal disease. Circ Res 115: 857-866.
40. Zhang Y, Fan M, Zhang X, Huang F, Wu K, Zhang J, Liu J, Huang Z, Luo H, Tao L, et al. 2014. Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs. RNA 20: 1878-1889.
41. Zhu W, Yang L, Du Z. 2011. MicroRNA regulation and tissue-specific protein interaction network. PLoS One 6: e25394.