Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Ribeiro dos Santos, Ândrea ^a   Khayat, André S ^a   Silva, Artur ^a   Alencar, Dayse O ^a   Lobato, Jessé ^a   Luz, Larissa ^a   Pinheiro, Daniel G ^b   Varuzza, Leonardo ^c   Assumpção, Monica ^a   Assumpção, Paulo ^a   Santos, Sidney ^a   Zanette, Dalila L ^b,d   Silva Jr , Wilson A ^b,d   Burbano, Rommel ^a   Darnet, Sylvain ^a  

^a FEDERAL UNIVERSITY OF PARÁ   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c Life Technologies   (Brazil)

^d Instituto Nacional de Ciência e Tecnologia   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 148A; MICRORNA 19B; MICRORNA 29B; MICRORNA 29C; MICRORNA 31; MICRORNA 451; UNCLASSIFIED DRUG;

ADULT; ARTICLE; CARDIA; CONTROLLED STUDY; FEMALE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE LIBRARY; GENE TARGETING; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; STOMACH; TRANSLATION REGULATION; GENETICS; METABOLISM;

GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; STOMACH;

EID: 78149432202     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013205     Document Type: Article

References (28)

1. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
2. Ricarte Filho JC, Kimura ET (2006) MicroRNAs: novel class of gene regulators involved in endocrine function and cancer. Arq Bras Endocrinol Metabol 50: 1102-1107.
3. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Siomi H, Siomi MC (2010) Posttranscriptional regulation of microRNA biogenesis in animals. Mol Cell 38: 323-332.
5. Croce CM (2009) Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet 10: 704-714.
6. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
7. Meltzer PS (2005) Cancer genomics: small RNAs with big impacts. Nature 435: 745-746.
8. Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM (2009) MiRanalyzer: a microRNA detection and analysis tool for nextgeneration sequencing experiments. Nucleic Acids Res 37: W68-76.
9. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) MiRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-4.
10. Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36: D149-53.
11. Kuehn H, Liberzon A, Reich M, Mesirov JP (2008) Using GenePattern for gene expression analysis. Curr Protoc Bioinformatics Chapter 7: Unit 7.12.
12. Fischbach W, Malfertheiner P, Hoffmann JC, Bolten W, Kist M, et al. (2009) Association of Scientific Medical Societies. Helicobacter pylori and gastroduodenal ulcer disease. Dtsch Arztebl Int 106(49): 801-8.
13. Langner M, Machado RS, Patrício FR, Kawakami E (2009) Evaluation of gastric histology in children and adolescents with Helicobacter pylori gastritis using the Update Sydney System. Arq Gastroenterol 46(4): 328-32.
14. Olive V, Bennett MJ, Walker JC, Ma C, Jiang I, Cordon-Cardo C, et al. (2009) MiR-19 is a key oncogenic component of mir-17-92. Gene Dev 23: 2839-2849.
15. Magoha GA (2007) Overview of prostate cancer in indigenous black Africans and blacks of African ancestry in diaspora 1935-2007. East Afr Med J 84: S3-11.
16. Chen Y, Souaiaia T, Chen T (2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25: 2514-2521.
17. Liang Y, Ridzon D, Wong L, Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8: 166-187.
18. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
19. Merkerova M, Vasikova A, Belickova M, Bruchova H (2010) MicroRNA expression profiles in umbilical cord blood cell lineages. Stem Cells Dev 19: 17-26.
20. Lujambio A, Calin GA, Villanueva A, Ropero S, Sanchez-Cespedes M, et al. (2008) A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci USA 105: 13556-13561.
21. Hu X, Macdonald DM, Huettner PC, Feng Z, El Naqa IM, et al. (2009) A miR-200 microRNA cluster as prognostic marker in advanced ovarian cancer. Gynecol Oncol 114: 457-464.
22. Korpal M, Lee ES, Hu G, Kang Y (2008) The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2. J Biol Chem 30: 283(22): 14910-14914.
23. Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857-866.
24. Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, et al. (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA 101: 11755-11760.
25. Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, et al. (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67: 2456-2468.
26. Zhang Y, Li M, Wang H, Fisher WE, Lin PH, et al. (2009) Profiling of 95 miRNAs in Pancreatic cancer cell lines and surgical specimens by real-time PCR analysis. Word J Surg 33: 698-709.
27. Gibbons DL, Lin W, Creighton CJ, Rizvi ZH, Gregory PA, et al. (2009) Contextual extracellular cues promote tumor cell EMT and metastasis by regulating miR-200 family expression. Genes and Development 23: 2140-2151.
28. Merkerova M, Vasikova A, Belickova M, Bruchova H (2010) MicroRNA expression profiles in umbilical cord blood cell lineages. Stem Cells and Development 19(1): 17-25.