Dietary microRNA database (DMD): An archive database and analytic tool for food-borne microRNAs

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Chiang, Kevin ^a   Shu, Jiang ^a   Zempleni, Janos ^b   Cui, Juan ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 29B;

ANALYTIC METHOD; APPLE; ARTICLE; DATA BASE; DIETARY MICRORNA DATABASE; ENTROPY; FOOD; GENE TARGETING; GRAPE; HIGH THROUGHPUT SCREENING; HUMAN; MACHINE LEARNING; MILK; NUTRITIONAL ASSESSMENT; PREDICTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; SEQUENCE ALIGNMENT; WORKFLOW; ANIMAL; BOVINE; DIET; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; NUCLEOTIDE SEQUENCE;

ANIMALIA; MALUS X DOMESTICA; VITACEAE;

ANIMALS; BASE SEQUENCE; CATTLE; DATABASES, GENETIC; DIET; FOOD; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS;

EID: 84934946413     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0128089     Document Type: Article

References (54)

1. Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med. 2005;353(17):1793-801. PMID: 16251535
2. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 2006;9(3):189-98. PMID: 16530703
3. Bloomston M, Frankel WL, Petrocca F, Volinia S, Alder H, Hagan JP, et al. MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA. 2007;297(17):1901-8. PMID: 17473300
4. Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, et al. MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA. 2008;299(4):425-36. doi: 10.1001/jama.299.4.425 PMID: 18230780
5. Garzon R, Volinia S, Liu CG, Fernandez-Cymering C, Palumbo T, Pichiorri F, et al. MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. Blood. 2008;111(6):3183-9. doi: 10.1182/blood-2007-07-098749 PMID: 18187662
6. Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O'Briant K, Godwin AK, et al. Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One. 2009;4(4):e5311. doi: 10.1371/journal.pone.0005311 PMID: 19390579
7. Ambs S, Prueitt RL, Yi M, Hudson RS, Howe TM, Petrocca F, et al. Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. Cancer Res. 2008;68(15):6162-70. doi: 10.1158/0008-5472. CAN-08-0144 PMID: 18676839
8. Croce CM. Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet. 2009;10(10):704-14. doi: 10.1038/nrg2634 PMID: 19763153
9. Griffiths-Jones S. miRBase: microRNA sequences and annotation. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al]. 2010; Chapter 12: Unit 12 9 1-0.
10. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic acids research. 2009;37(Database issue):D105-10. doi: 10.1093/nar/gkn851 PMID: 18996891
11. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120(1):15-20. PMID: 15652477
12. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell. 2006;126(6):1203-17. PMID: 16990141
13. Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, et al. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic acids research. 2014;42(Database issue):D78-85. doi: 10.1093/nar/gkt1266 PMID: 24304892
14. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281-97. PMID: 14744438
15. Ambros V. The functions of animal microRNAs. Nature. 2004;431(7006):350-5. PMID: 15372042
16. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic acids research. 2002;30(1):207-10. PMID: 11752295
17. Tomczak K, Czerwinska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemporary oncology. 2015;19(1 A):A68-77. doi: 10.5114/wo.2014.47136 PMID: 25691825
18. Chen X, Gao C, Li H, Huang L, Sun Q, Dong Y, et al. Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products. Cell Res. 2010;20(10):1128-37. doi: 10.1038/cr.2010.80 PMID: 20548333
19. Wang H, Zheng Y, Wang G, Li H. Identification of microRNA and bioinformatics target gene analysis in beef cattle intramuscular fat and subcutaneous fat. Molecular bioSystems. 2013;9(8):2154-62. doi: 10. 1039/c3mb70084d PMID: 23728155
20. Weber JA, Baxter DH, Zhang S, Huang DY, Huang KH, Lee MJ, et al. The microRNA spectrum in 12 body fluids. Clinical chemistry. 2010;56(11):1733-41. doi: 10.1373/clinchem.2010.147405 PMID: 20847327
21. Baier SR, Nguyen C, Xie F, Wood JR, Zempleni J. MicroRNAs are absorbed in biologically meaningful amounts from nutritionally relevant doses of cow milk and affect gene expression in peripheral blood mononuclear cells, HEK-293 kidney cell cultures, and mouse livers. J Nutr. 2014;144(10):1495-500. doi: 10.3945/jn. 114.196436 PMID: 25122645
22. Izumi H, Kosaka N, Shimizu T, Sekine K, Ochiya T, Takase M. Bovine milk contains microRNA and messenger RNA that are stable under degradative conditions. J Dairy Sci. 2012;95(9):4831-41. doi: 10.3168/jds.2012-5489 PMID: 22916887
23. Arnold CN, Pirie E, Dosenovic P, McInerney GM, Xia Y, Wang N, et al. A forward genetic screen reveals roles for Nfkbid, Zeb1, and Ruvbl2 in humoral immunity. Proc Natl Acad Sci U S A. 2012;109(31):12286-93. doi: 10.1073/pnas.1209134109 PMID: 22761313
24. Liu R, Ma X, Xu L, Wang D, Jiang X, Zhu W, et al. Differential microRNA expression in peripheral blood mononuclear cells from Graves' disease patients. J Clin Endocrinol Metab. 2012;97(6):E968-72. doi: 10.1210/jc.2011-2982 PMID: 22456620
25. Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, et al. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res. 2012;22(1):107-26. doi: 10.1038/cr.2011.158 PMID: 21931358
26. Snow JW, Hale AE, Isaacs SK, Baggish AL, Chan SY. Ineffective delivery of diet-derived microRNAs to recipient animal organisms. RNA biology. 2013;10(7):1107-16. Epub 2013/05/15. doi: 10.4161/rna. 24909 PMID: 23669076
27. Dickinson B, Zhang Y, Petrick JS, Heck G, Ivashuta S, Marshall WS. Lack of detectable oral bioavailability of plant microRNAs after feeding in mice. Nature biotechnology. 2013;31(11):965-7. doi: 10. 1038/nbt.2737 PMID: 24213763
28. Chen X, Zen K, Zhang CY. Reply to Lack of detectable oral bioavailability of plant microRNAs after feeding in mice. Nature biotechnology. 2013;31(11):967-9. Epub 2013/11/12. doi: 10.1038/nbt.2741 PMID: 24213764
29. Wang K, Li H, Yuan Y, Etheridge A, Zhou Y, Huang D, et al. The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS ONE. 2012;7(12):e51009. doi: 10.1371/journal.pone.0051009 PMID: 23251414
30. Gomes CP, Cho JH, Hood L, Franco OL, Pereira RW, Wang K. A Review of Computational Tools in microRNA Discovery. Frontiers in genetics. 2013;4:81. doi: 10.3389/fgene.2013.00081 PMID: 23720668
31. Leclercq M, Diallo AB, Blanchette M. Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic acids research. 2013;41(15):7200-11. doi: 10.1093/nar/gkt466 PMID: 23748953
32. Batuwita R, Palade V. microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics. 2009;25(8):989-95. doi: 10.1093/bioinformatics/btp107 PMID: 19233894
33. Wang H, Xiao S, Wang M, Kim NH, Li H, Wang G. In silico identification of conserved microRNAs and their targets in bovine fat tissue. Gene. 2015;559(2):119-28. doi: 10.1016/j.gene.2015.01.021 PMID: 25626178
34. Xuan P, Han K, Guo Y, Li J, Li X, Zhong Y, et al. Prediction of potential disease-associated microRNAs based on random walk. Bioinformatics. 2015
35. Blevins R, Bruno L, Carroll T, Elliott J, Marcais A, Loh C, et al. microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes. PLoS genetics. 2015;11(2):e1005020. doi: 10.1371/journal.pgen. 1005020 PMID: 25714103
36. Cui J, Eldredge JB, Xu Y, Puett D. MicroRNA expression and regulation in human ovarian carcinoma cells by luteinizing hormone. PLoS One. 2011;6(7):e21730. doi: 10.1371/journal.pone.0021730 PMID: 21765906
37. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150-2. doi: 10.1093/bioinformatics/bts565 PMID: 23060610
38. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic acids research. 2011;39(Database issue):D163-9. doi: 10.1093/nar/gkq1107 PMID: 21071411
39. Wang X, El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics. 2008;24(3):325-32. PMID: 18048393
40. Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic acids research. 2011;39(Web Server issue):W155-9. doi: 10.1093/nar/gkr319 PMID: 21622958
41. Aoki KF, Kanehisa M. Using the KEGG database resource. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al]. 2005; Chapter 1: Unit 1 12.
42. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic acids research. 2006;34(Database issue):D535-9. PMID: 16381927
43. Lopes Ide O, Schliep A, de Carvalho AC. The discriminant power of RNA features for pre-miRNA recognition. BMC Bioinformatics. 2014;15:124. doi: 10.1186/1471-2105-15-124 PMID: 24884650
44. Xuan P, Guo M, Liu X, Huang Y, Li W, Huang Y. PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs. Bioinformatics. 2011;27(10):1368-76. doi: 10.1093/bioinformatics/btr153 PMID: 21441575
45. Mathelier A, Carbone A. Large scale chromosomal mapping of human microRNA structural clusters. Nucleic acids research. 2013;41(8):4392-408. doi: 10.1093/nar/gkt112 PMID: 23444140
46. Lertampaiporn S, Thammarongtham C, Nukoolkit C, Kaewkamnerdpong B, Ruengjitchatchawalya M. Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm. Nucleic acids research. 2014;42(11):e93. doi: 10.1093/nar/gku325 PMID: 24771344
47. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31(13):3429-31. PMID: 12824340
48. Denman RB. Using RNAFOLD to predict the activity of small catalytic RNAs. BioTechniques. 1993;15(6):1090-5. PMID: 8292343
49. Janssen S, Giegerich R. The RNA shapes studio. Bioinformatics. 2015;31(3):423-5. doi: 10.1093/bioinformatics/btu649 PMID: 25273103
50. Knudsen V, Caetano-Anolles G. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure. Nucleic acids research. 2008;36(Web Server issue):W85-90. doi: 10. 1093/nar/gkn220 PMID: 18448469
51. Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2006;22(4):500-3. PMID: 16357029
52. Li Y, Qiu C, Tu J, Geng B, Yang J, Jiang T, et al. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic acids research. 2014;42(Database issue):D1070-4. doi: 10.1093/nar/gkt1023 PMID: 24194601
53. Ruepp A, Kowarsch A, Theis F. PhenomiR: microRNAs in human diseases and biological processes. Methods in molecular biology. 2012;822:249-60. doi: 10.1007/978-1-61779-427-8-17 PMID: 22144204
54. Schulz MH, Pandit KV, Lino Cardenas CL, Ambalavanan N, Kaminski N, Bar-Joseph Z. Reconstructing dynamic microRNA-regulated interaction networks. Proc Natl Acad Sci U S A. 2013;110(39):15686-91. doi: 10.1073/pnas.1303236110 PMID: 23986498