DbDEMC: A database of differentially expressed miRNAs in human cancers

BMC Genomics

Volumn 11, Issue SUPPL. 4, 2010, Pages

  Yang, Zhen ^a,b,c   Ren, Fei ^b   Liu, Changning ^b   He, Shunmin ^d   Sun, Gang ^e   Gao, Qian ^e   Yao, Lei ^a   Zhang, Yangde ^f   Miao, Ruoyu ^c   Cao, Ying ^g,h   Zhao, Yi ^b   Zhong, Yang ^a,i   Zhao, Haitao ^c  

^a FUDAN UNIVERSITY   (China)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c PEKING UNION MEDICAL COLLEGE HOSPITAL   (China)

^d INSTITUTE OF ZOOLOGY   (China)

^e FUDAN UNIVERSITY   (China)

^f CENTRAL SOUTH UNIVERSITY   (China)

^g INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^h GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

ⁱ SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MESSENGER RNA; SMALL UNTRANSLATED RNA; TUMOR MARKER;

APOPTOSIS; ARTICLE; CANCER CELL; CANCER CLASSIFICATION; CANCER RESEARCH; CELL DIFFERENTIATION; CELL DIVISION; CELL PROLIFERATION; COMPUTER PROGRAM; DATABASE OF DIFFERENTIALLY EXPRESSED MIRNAS IN HUMAN CANCERS; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC IDENTIFICATION; HUMAN; INFORMATION PROCESSING; INTERNET; MICROARRAY ANALYSIS; PEER REVIEW; COMPARATIVE STUDY; FACTUAL DATABASE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; NEOPLASM; PHYSIOLOGY; REPRODUCIBILITY; RNA PROCESSING; STATISTICAL ANALYSIS; STATISTICS; UTILIZATION REVIEW;

DATA INTERPRETATION, STATISTICAL; DATABASES, FACTUAL; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INTERNET; MICROARRAY ANALYSIS; MICRORNAS; NEOPLASMS; REPRODUCIBILITY OF RESULTS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; TUMOR MARKERS, BIOLOGICAL;

BIOLOGICAL PROCESS; CELL DIVISIONS; DATA SETS; EMBRYONIC DEVELOPMENT; EXPRESSION LEVELS; EXPRESSION PROFILE; HUMAN CANCER; HUMAN DISEASE; MICROARRAY DATA SETS; MICRORNAS; NON-CODING RNAS; NORMAL TISSUE; POST-TRANSCRIPTIONAL; SIGNIFICANCE ANALYSIS OF MICROARRAYS; WEB INTERFACE;

CELL DEATH; CELL PROLIFERATION; DATABASE SYSTEMS; DIAGNOSIS; DISEASES; MICROARRAYS; RNA; TISSUE; TRANSCRIPTION;

BIOINFORMATICS;

EID: 78649778244     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S4-S5     Document Type: Article

References (45)

1. Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, Cole C, Kok CY, Jia M, Ewing R, Menzies A, et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res 2010, 38(Database issue):D652-657. 10.1093/nar/gkp995, 2808858, 19906727.
2. Elfilali A, Lair S, Verbeke C, La Rosa P, Radvanyi F, Barillot E. ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res 2006, 34(Database issue):D613-616. 10.1093/nar/gkj022, 1347385, 16381943.
3. Wang X, Zhao H, Xu Q, Jin W, Liu C, Zhang H, Huang Z, Zhang X, Zhang Y, Xin D, et al. HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. Nucleic Acids Res 2006, 34(Database issue):D607-612. 10.1093/nar/gkj082, 1347445, 16381942.
4. Li H, He Y, Ding G, Wang C, Xie L, Li Y. dbDEPC: a database of differentially expressed proteins in human cancers. Nucleic Acids Res 2010, 38(Database issue):D658-664. 10.1093/nar/gkp933, 2808941, 19900968.
5. Vandenboom Ii TG, Li Y, Philip PA, Sarkar FH. MicroRNA and Cancer: Tiny Molecules with Major Implications. Curr Genomics 2008, 9(2):97-109. 10.2174/138920208784139555, 2674802, 19440450.
6. Gregory RI, Shiekhattar R. MicroRNA biogenesis and cancer. Cancer Res 2005, 65(9):3509-3512. 10.1158/0008-5472.CAN-05-0298, 15867338.
7. DeSano JT, Xu L. MicroRNA regulation of cancer stem cells and therapeutic implications. Aaps J 2009, 11(4):682-692. 10.1208/s12248-009-9147-7, 2782081, 19842044.
8. Sassen S, Miska EA, Caldas C. MicroRNA: implications for cancer. Virchows Arch 2008, 452(1):1-10. 10.1007/s00428-007-0532-2, 2151131, 18040713.
9. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
10. He S, Yang Z, Skogerbo G, Ren F, Cui H, Zhao H, Chen R, Zhao Y. The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs. Crit Rev Microbiol 2008, 34(3-4):175-188. 10.1080/10408410802482008, 18972284.
11. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 2005, 434(7031):338-345. 10.1038/nature03441, 2923337, 15735639.
12. Cheng AM, Byrom MW, Shelton J, Ford LP. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res 2005, 33(4):1290-1297. 10.1093/nar/gki200, 552951, 15741182.
13. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH. MicroRNA expression in zebrafish embryonic development. Science 2005, 309(5732):310-311. 10.1126/science.1114519, 15919954.
14. Alvarez-Garcia I, Miska EA. MicroRNA functions in animal development and human disease. Development 2005, 132(21):4653-4662. 10.1242/dev.02073, 16224045.
15. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 2002, 99(24):15524-15529. 10.1073/pnas.242606799, 137750, 12434020.
16. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, et al. A microRNA polycistron as a potential human oncogene. Nature 2005, 435(7043):828-833. 10.1038/nature03552, 15944707.
17. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 2005, 435(7043):839-843. 10.1038/nature03677, 15944709.
18. Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K, Tomida S, Yatabe Y, Kawahara K, Sekido Y, Takahashi T. A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 2005, 65(21):9628-9632. 10.1158/0008-5472.CAN-05-2352, 16266980.
19. Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y, et al. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 2004, 64(11):3753-3756. 10.1158/0008-5472.CAN-04-0637, 15172979.
20. Kutay H, Bai S, Datta J, Motiwala T, Pogribny I, Frankel W, Jacob ST, Ghoshal K. Downregulation of miR-122 in the rodent and human hepatocellular carcinomas. J Cell Biochem 2006, 99(3):671-678. 10.1002/jcb.20982, 16924677.
21. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 2004, 101(9):2999-3004. 10.1073/pnas.0307323101, 365734, 14973191.
22. Zhao JJ, Yang J, Lin J, Yao N, Zhu Y, Zheng J, Xu J, Cheng JQ, Lin JY, Ma X. Identification of miRNAs associated with tumorigenesis of retinoblastoma by miRNA microarray analysis. Childs Nerv Syst 2009, 25(1):13-20. 10.1007/s00381-008-0701-x, 18818933.
23. Fan AC, Goldrick MM, Ho J, Liang Y, Bachireddy P, Felsher DW. A quantitative PCR method to detect blood microRNAs associated with tumorigenesis in transgenic mice. Mol Cancer 2008, 7(1):74. 10.1186/1476-4598-7-74, 2572631, 18826639.
24. Ge X, Wu Q, Wang SM. SAGE detects microRNA precursors. BMC Genomics 2006, 7:285. 10.1186/1471-2164-7-285, 1636050, 17090314.
25. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, et al. MicroRNA expression profiles classify human cancers. Nature 2005, 435(7043):834-838. 10.1038/nature03702, 15944708.
26. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36(Database issue):D149-153. 2238905, 18158296.
27. Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 2008, 36(Database issue):D159-164. 2238850, 17942429.
28. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. miR2 Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2008, 2686559, 18927107.
29. Sarver AL, Phalak R, Thayanithy V, Subramanian S. S-MED: sarcoma microRNA expression database. Lab Invest 90(5):753-761. 10.1038/labinvest.2010.53, 20212452.
30. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, 37(Database issue):D885-890. 10.1093/nar/gkn764, 2686538, 18940857.
31. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98(9):5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
32. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36(Database issue):D154-158. 2238936, 17991681.
33. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004, 2(11):e363. 10.1371/journal.pbio.0020363, 521178, 15502875.
34. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37(5):495-500. 10.1038/ng1536, 15806104.
35. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115(7):787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
36. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
37. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 2004, 101(25):9309-9314. 10.1073/pnas.0401994101, 438973, 15184677.
38. Xia L, Zhang D, Du R, Pan Y, Zhao L, Sun S, Hong L, Liu J, Fan D. miR-15b and miR-16 modulate multidrug resistance by targeting BCL2 in human gastric cancer cells. Int J Cancer 2008, 123(2):372-379. 10.1002/ijc.23501, 18449891.
39. Slaby O, Svoboda M, Fabian P, Smerdova T, Knoflickova D, Bednarikova M, Nenutil R, Vyzula R. Altered expression of miR-21, miR-31, miR-143 and miR-145 is related to clinicopathologic features of colorectal cancer. Oncology 2007, 72(5-6):397-402. 10.1159/000113489, 18196926.
40. Akao Y, Nakagawa Y, Kitade Y, Kinoshita T, Naoe T. Downregulation of microRNAs-143 and -145 in B-cell malignancies. Cancer Sci 2007, 98(12):1914-1920. 10.1111/j.1349-7006.2007.00618.x, 17892514.
41. Schimanski CC, Frerichs K, Rahman F, Berger M, Lang H, Galle PR, Moehler M, Gockel I. High miR-196a levels promote the oncogenic phenotype of colorectal cancer cells. World J Gastroenterol 2009, 15(17):2089-2096. 10.3748/wjg.15.2089, 2678579, 19418581.
42. Maru DM, Singh RR, Hannah C, Albarracin CT, Li YX, Abraham R, Romans AM, Yao H, Luthra MG, Anandasabapathy S, et al. MicroRNA-196a is a potential marker of progression during Barrett's metaplasia-dysplasia-invasive adenocarcinoma sequence in esophagus. Am J Pathol 2009, 174(5):1940-1948. 10.2353/ajpath.2009.080718, 2671281, 19342367.
43. Guttilla IK, White BA. Coordinate regulation of FOXO1 by miR-27a, miR-96, and miR-182 in breast cancer cells. J Biol Chem 2009, 284(35):23204-23216. 10.1074/jbc.M109.031427, 2749094, 19574223.
44. Li W, Duan R, Kooy F, Sherman SL, Zhou W, Jin P. Germline mutation of microRNA-125a is associated with breast cancer. J Med Genet 2009, 46(5):358-360. 10.1136/jmg.2008.063123, 19411564.
45. Zhao JJ, Lin J, Yang H, Kong W, He L, Ma X, Coppola D, Cheng JQ. MicroRNA-221/222 negatively regulates estrogen receptor alpha and is associated with tamoxifen resistance in breast cancer. J Biol Chem 2008, 283(45):31079-31086. 10.1074/jbc.M806041200, 2576549, 18790736.