Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis

Molecular Neurobiology

Volumn 45, Issue 3, 2012, Pages 520-535

  Angerstein, Charlotte ^a   Hecker, Michael ^a   Paap, Brigitte Katrin ^a   Koczan, Dirk ^a   Thamilarasan, Madhan ^a   Thiesen, Hans Jürgen ^a   Zettl, Uwe Klaus ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

Author keywords

Databases; Gene regulatory networks; MicroRNA; Multiple sclerosis

Indexed keywords

MICRORNA;

ARTICLE; BLOOD; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; MULTIPLE SCLEROSIS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY;

BASE SEQUENCE; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; MULTIPLE SCLEROSIS; REPRODUCIBILITY OF RESULTS;

EID: 84867478229     PISSN: 08937648     EISSN: 15591182     Source Type: Journal    
DOI: 10.1007/s12035-012-8270-0     Document Type: Article

References (127)

1. Compston A, Coles A (2008) Multiple sclerosis. Lancet 372 (9648):1502-1517
2. Lassmann H, Brück W, Lucchinetti CF (2007) The immunopathology of multiple sclerosis: an overview. Brain Pathol 17 (2):210-218
3. Sospedra M, Martin R (2005) Immunology of multiple sclerosis. Annu Rev Immunol 23:683-747
4. Goertsches RH, Hecker M, Zettl UK (2008) Monitoring of multiple sclerosis immunotherapy: from single candidates to biomarker networks. J Neurol 255(Suppl 6):48-57
5. Goertsches RH, Zettl UK, Hecker M (2011) Sieving treatment biomarkers from blood gene-expression profiles: a pharmacogenomic update on two types of multiple sclerosis therapy. Pharmacogenomics 12(3):423-432
6. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843-854
7. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853-858
8. Ha TY (2011) MicroRNAs in human diseases: from cancer to cardiovascular disease. Immune Netw 11(3):135-154
9. Liu Z, Sall A, Yang D (2008) MicroRNA: an emerging therapeutic target and intervention tool. Int J Mol Sci 9(6):978-999
10. Guerau-de-Arellano M, Alder H, Ozer HG, Lovett-Racke A, Racke MK (2011) miRNA profiling for biomarker discovery in multiple sclerosis: from microarray to deep sequencing. J Neuroimmunol. doi:10.1016/j.jneuroim.2011.10.006
11. Junker A (2011) Pathophysiology of translational regulation by microRNAs in multiple sclerosis. FEBS Lett 585(23):3738-3746
12. Thamilarasan M, Koczan D, Hecker M, Paap B, Zettl UK (2012) MicroRNAs in multiple sclerosis and experimental autoimmune encephalomyelitis. Autoimmun Rev 11(3):174-179
13. Tufekci KU, Oner MG, Genc S, Genc K (2010) MicroRNAs and multiple sclerosis. Autoimmune Dis 2011:807426
14. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281-297
15. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue): D140-D144
16. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9(2):102-114
17. Jinek M, Doudna JA (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature 457(7228): 405-412
18. Kim YK, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26(3):775-783
19. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1):92-105
20. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG (2009) Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25(23):3049-3055
21. Mazière P, Enright AJ (2007) Prediction of microRNA targets. Drug Discov Today 12(11-12):452-458
22. Yue D, Liu H, Huang Y (2009) Survey of computational algorithms for microRNA target prediction. Curr Genomics 10 (7):478-492
23. Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG (2010) miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 38(Database issue):D137-D141
24. Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36(Database issue):D149-D153
25. Dweep H, Sticht C, Pandey P, Gretz N (2011) miRWalk - database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 44(5):839-847
26. Friard O, Re A, Taverna D, De Bortoli M, Corá D (2010) CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinformatics 11:435
27. Gong J, Tong Y, Zhang HM, Wang K, Hu T, Shan G, Sun J, Guo AY (2012) Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum Mutat 33(1):254-263
28. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36 (Database issue):D154-D158
29. Grün D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1(1):e13
30. Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M (2009) MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res 37(Web Server issue):W266-W272
31. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH,Wu MC, Huang CY, Tsou AP, Huang HD (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39(Database issue):D163-D169
32. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37 (Database issue):D98-D104
33. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39(Database issue):D152-D157
34. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005) Combinatorial microRNA target predictions. Nat Genet 37(5):495-500
35. Lall S, Grün D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N (2006) A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 16(5):460-471
36. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115 (7):787-798
37. Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q (2008) An analysis of human microRNA and disease associations. PLoS One 3(10):e3420
38. Maragkakis M, Vergoulis T, Alexiou P, Reczko M, Plomaritou K, Gousis M, Kourtis K, Koziris N, Dalamagas T, Hatzigeorgiou AG (2011) DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Res 39(Web Server issue): W145-W148
39. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 37(Database issue):D155-D158
40. Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis FJ (2010) PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol 11(1):R6
41. Wang X (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14 (6):1012-1017
42. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37(Database issue):D105-D110
43. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS (2003) MicroRNA targets in Drosophila. Genome Biol 5(1):R1
44. Lytle JR, Yario TA, Steitz JA (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci U S A 104(23):9667-9672
45. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A 105(5):1608-1613
46. Schnall-Levin M, Rissland OS, Johnston WK, Perrimon N, Bartel DP, Berger B (2011) Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res 21(9):1395-1403
47. Al-Shahrour F,Minguez P, Tárraga J,Medina I, Alloza E,Montaner D, Dopazo J (2007) FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35(Web Server issue):W91-W96
48. Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J (2010) Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res 38(Web Server issue):W210-W213
49. Liang Y, Ridzon D, Wong L, Chen C (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8:166
50. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401-1414
51. Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31 (13):3576-3579
52. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüss M, Reuter I, Schacherer F (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28(1):316-319
53. Cox MB, Cairns MJ, Gandhi KS, Carroll AP, Moscovis S, Stewart GJ, Broadley S, Scott RJ, Booth DR, Lechner-Scott J, ANZ gene multiple sclerosis genetics consortium (2010) MicroRNAs miR-17 and miR-20a inhibit T cell activation genes and are under-expressed inMS whole blood. PLoS One 5(8): e12132
54. Du C, Liu C, Kang J, Zhao G, Ye Z, Huang S, Li Z, Wu Z, Pei G (2009) MicroRNA miR-326 regulates TH-17 differentiation and is associated with the pathogenesis ofmultiple sclerosis. Nat Immunol 10(12):1252-1259
55. Keller A, Leidinger P, Lange J, Borries A, Schroers H, Scheffler M, Lenhof HP, Ruprecht K, Meese E (2009) Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One 4(10):e7440
56. Keller A, Leidinger P, Bauer A, Elsharawy A, Haas J, Backes C, Wendschlag A, Giese N, Tjaden C, Ott K, Werner J, Hackert T, Ruprecht K, Huwer H, Huebers J, Jacobs G, Rosenstiel P, Dommisch H, Schaefer A, Müller-Quernheim J, Wullich B, Keck B, Graf N, Reichrath J, Vogel B, Nebel A, Jager SU, Staehler P, Amarantos I, Boisguerin V, Staehler C, Beier M, Scheffler M, Büchler MW, Wischhusen J, Haeusler SF, Dietl J, Hofmann S, Lenhof HP, Schreiber S, Katus HA, Rottbauer W, Meder B, Hoheisel JD, Franke A, Meese E (2011) Toward the blood-borne miRNome of human diseases. Nat Methods 8 (10):841-843
57. Otaegui D, Baranzini SE, Armañanzas R, Calvo B, Muñoz-Culla M, Khankhanian P, Inza I, Lozano JA, Castillo-Triviño T, Asensio A, Olaskoaga J, López deMunainA (2009) Differential micro RNA expression in PBMC from multiple sclerosis patients. PLoS One 4 (7):e6309
58. Saini HK, Enright AJ, Griffiths-Jones S (2008) Annotation of mammalian primary microRNAs. BMC Genomics 9:564
59. Xiao C, Srinivasan L, Calado DP, Patterson HC, Zhang B, Wang J, Henderson JM, Kutok JL, Rajewsky K (2008) Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol 9(4):405-414
60. Landais S, Landry S, Legault P, Rassart E (2007) Oncogenic potential of the miR-106-363 cluster and its implication in human T-cell leukemia. Cancer Res 67(12):5699-5707
61. Ventura A, Young AG, Winslow MM, Lintault L, Meissner A, Erkeland SJ, Newman J, Bronson RT, Crowley D, Stone JR, Jaenisch R, Sharp PA, Jacks T (2008) Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 132(5):875-886
62. Junker A, Hohlfeld R, Meinl E (2011) The emerging role of microRNAs in multiple sclerosis. Nat Rev Neurol 7(1):56-59
63. Noorbakhsh F, Ellestad KK, Maingat F, Warren KG, Han MH, Steinman L, Baker GB, Power C (2011) Impaired neurosteroid synthesis in multiple sclerosis. Brain 134(Pt 9):2703-2721
64. De Santis G, Ferracin M, Biondani A, Caniatti L, Rosaria Tola M, Castellazzi M, Zagatti B, Battistini L, Borsellino G, Fainardi E, Gavioli R, Negrini M, Furlan R, Granieri E (2010) Altered miRNA expression in T regulatory cells in course of multiple sclerosis. J Neuroimmunol 226(1-2):165-171
65. Lindberg RL, Hoffmann F, Mehling M, Kuhle J, Kappos L (2010) Altered expression of miR-17-5p in CD4+ lymphocytes of relapsing-remitting multiple sclerosis patients. Eur J Immunol 40(3):888-898
66. Fenoglio C, Cantoni C, De Riz M, Ridolfi E, Cortini F, Serpente M, Villa C, Comi C, Monaco F, Mellesi L, Valzelli S, Bresolin N, Galimberti D, Scarpini E (2011) Expression and genetic analysis of miRNAs involved in CD4+ cell activation in patients with multiple sclerosis. Neurosci Lett 504(1):9-12
67. Lorenzi JC, Brum DG, Zanette DL, Souza AD, Barbuzano FG, Santos AC, Barreira AA, Silva WA Jr (2012) miR-15a and 16-1 are downregulated in CD4(+) T cells of multiple sclerosis relapsing patients. Int J Neurosci. doi:10.3109/00207454.2012.678444
68. Siegel SR, Mackenzie J, Chaplin G, Jablonski NG, Griffiths L (2012) Circulating microRNAs involved in multiple sclerosis. Mol Biol Rep 39(5):6219-6225
69. Paraboschi EM, Soldà G, Gemmati D, Orioli E, Zeri G, Benedetti MD, Salviati A, Barizzone N, Leone M, Duga S, Asselta R (2011) Genetic association and altered gene expression of mir-155 in multiple sclerosis patients. Int J Mol Sci 12(12):8695-8712
70. Martinelli-Boneschi F, Fenoglio C, Brambilla P, Sorosina M, Giacalone G, Esposito F, Serpente M, Cantoni C, Ridolfi E, Rodegher M, Moiola L, Colombo B, De Riz M, Martinelli V, Scarpini E, Comi G, Galimberti D (2012) MicroRNA and mRNA expression profile screening in multiple sclerosis patients to unravel novel pathogenic steps and identify potential biomarkers. Neurosci Lett 508(1):4-8
71. Guerau-de-Arellano M, Smith KM, Godlewski J, Liu Y, Winger R, Lawler SE, Whitacre CC, Racke MK, Lovett-Racke AE (2011) Micro-RNA dysregulation in multiple sclerosis favours proinflammatory T-cell-mediated autoimmunity. Brain 134(Pt 12):3575-3586
72. Waschbisch A, Atiya M, Linker RA, Potapov S, Schwab S, Derfuss T (2011) Glatiramer acetate treatment normalizes deregulated microRNA expression in relapsing remitting multiple sclerosis. PLoS One 6(9):e24604
73. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3):431-432
74. Lekprasert P, Mayhew M, Ohler U (2011) Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements. PLoS One 6(6): e20622
75. Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG (2011) Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data. Front Genet 2:103
76. Mahony S, Benos PV (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35(Web Server issue):W253-W258
77. Kasper LH, Shoemaker J (2010) Multiple sclerosis immunology: the healthy immune system vs the MS immune system. Neurology 74(Suppl 1):S2-S8
78. Santiago-Raber ML, Lawson BR, Dummer W, Barnhouse M, Koundouris S, Wilson CB, Kono DH, Theofilopoulos AN (2001) Role of cyclin kinase inhibitor p21 in systemic autoimmunity. J Immunol 167(7):4067-4074
79. Wong WF, Kohu K, Chiba T, Sato T, Satake M (2011) Interplay of transcription factors in T-cell differentiation and function: the role of Runx. Immunology 132(2):157-164
80. Zhang F, Meng G, Strober W (2008) Interactions among the transcription factors Runx1, RORgammat and Foxp3 regulate the differentiation of interleukin 17-producing Tcells. Nat Immunol 9(11):1297-1306
81. Stittrich AB, Haftmann C, Sgouroudis E, Kühl AA, Hegazy AN, Panse I, Riedel R, Flossdorf M, Dong J, Fuhrmann F, Heinz GA, Fang Z, Li N, Bissels U, Hatam F, Jahn A, Hammoud B, Matz M, Schulze FM, Baumgrass R, Bosio A, Mollenkopf HJ, Grün J, Thiel A, Chen W, Höfer T, Loddenkemper C, Löhning M, Chang HD, Rajewsky N, Radbruch A, Mashreghi MF (2010) The micro-RNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes. Nat Immunol 11(11):1057-1062
82. Kerdiles YM, Stone EL, Beisner DR, McGargill MA, Ch'en IL, Stockmann C, Katayama CD, Hedrick SM (2010) Foxo transcription factors control regulatory T cell development and function. Immunity 33(6):890-904
83. DeRyckere D, DeGregori J (2005) E2F1 and E2F2 are differentially required for homeostasis-driven and antigen-induced T cell proliferation in vivo. J Immunol 175(2):647-655
84. Iglesias AH, Camelo S, Hwang D, Villanueva R, Stephanopoulos G, Dangond F (2004) Microarray detection of E2F pathway activation and other targets in multiple sclerosis peripheral blood mononuclear cells. J Neuroimmunol 150(1-2):163-177
85. Chaudhry A, Samstein RM, Treuting P, Liang Y, PilsMC, Heinrich JM, Jack RS,Wunderlich FT, Brüning JC,MüllerW, Rudensky AY (2011) Interleukin-10 signaling in regulatory T cells is required for suppression of Th17 cell-mediated inflammation. Immunity 34 (4):566-578
86. Durant L, Watford WT, Ramos HL, Laurence A, Vahedi G, Wei L, Takahashi H, Sun HW, Kanno Y, Powrie F, O'Shea JJ (2010) Diverse targets of the transcription factor STAT3 contribute to T cell pathogenicity and homeostasis. Immunity 32(5):605-615
87. Liu X, Lee YS, Yu CR, Egwuagu CE (2008) Loss of STAT3 in CD4+ T cells prevents development of experimental autoimmune diseases. J Immunol 180(9):6070-6076
88. Frisullo G, Nociti V, Iorio R, Patanella AK, Marti A, Mirabella M, Tonali PA, Batocchi AP (2008) The persistency of high levels of pSTAT3 expression in circulating CD4+ T cells from CIS patients favors the early conversion to clinically defined multiple sclerosis. J Neuroimmunol 205(1-2):126-134
89. Crispín JC, Tsokos GC (2009) Transcriptional regulation of IL-2 in health and autoimmunity. Autoimmun Rev 8(3):190-195
90. Grundström S, Anderson P, Scheipers P, Sundstedt A (2004) Bcl-3 and NFkappaB p50-p50 homodimers act as transcriptional repressors in tolerant CD4+ Tcells. J Biol Chem 279(9):8460-8468
91. Ullman KS, Flanagan WM, Edwards CA, Crabtree GR (1991) Activation of early gene expression in T lymphocytes by Oct-1 and an inducible protein, OAP40. Science 254(5031):558-562
92. Lichtinghagen R, Seifert T, Kracke A, Marckmann S, Wurster U, Heidenreich F (1999) Expression of matrix metalloproteinase-9 and its inhibitors in mononuclear blood cells of patients with multiple sclerosis. J Neuroimmunol 99(1):19-26
93. Rieckmann P, Albrecht M, Kitze B, Weber T, Tumani H, Broocks A, Lüer W, Helwig A, Poser S (1995) Tumor necrosis factoralpha messenger RNA expression in patients with relapsingremitting multiple sclerosis is associated with disease activity. Ann Neurol 37(1):82-88
94. Hilliard B, Samoilova EB, Liu TS, Rostami A, Chen Y (1999) Experimental autoimmune encephalomyelitis in NF-kappa Bdeficient mice:roles of NF-kappa B in the activation and differentiation of autoreactive T cells. J Immunol 163(5):2937-2943
95. Du C, Khalil MW, Sriram S (2001) Administration of dehydroepiandrosterone suppresses experimental allergic encephalomyelitis in SJL/J mice. J Immunol 167(12):7094-7101
96. van Loo G, De Lorenzi R, Schmidt H, Huth M, Mildner A, Schmidt-Supprian M, Lassmann H, Prinz MR, Pasparakis M (2006) Inhibition of transcription factor NF-kappaB in the central nervous system ameliorates autoimmune encephalomyelitis in mice. Nat Immunol 7(9):954-961
97. Vanderlugt CL, Rahbe SM, Elliott PJ, Dal Canto MC, Miller SD (2000) Treatment of established relapsing experimental autoimmune encephalomyelitis with the proteasome inhibitor PS-519. J Autoimmun 14(3):205-211
98. Bonetti B, Stegagno C, Cannella B, Rizzuto N, Moretto G, Raine CS (1999) Activation of NF-kappaB and c-jun transcription factors in multiple sclerosis lesions. Implications for oligodendrocyte pathology. Am J Pathol 155(5):1433-1438
99. Pfeuffer I, Klein-Hessling S, Heinfling A, Chuvpilo S, Escher C, Brabletz T, Hentsch B, Schwarzenbach H, Matthias P, Serfling E (1994) Octamer factors exert a dual effect on the IL-2 and IL-4 promoters. J Immunol 153(12):5572-5585
100. Bert AG, Burrows J, Hawwari A, Vadas MA, Cockerill PN (2000) Reconstitution of T cell-specific transcription directed by composite NFAT/Oct elements. J Immunol 165(10):5646-5655
101. Mordvinov VA, Schwenger GT, Fournier R, De Boer ML, Peroni SE, Singh AD, Karlen S, Holland JW, Sanderson CJ (1999) Binding of YY1 and Oct1 to a novel element that downregulates expression of IL-5 in human T cells. J Allergy Clin Immunol 103 (6):1125-1135
102. Wu GD, Lai EJ, Huang N, Wen X (1997) Oct-1 and CCAAT/ enhancer-binding protein (C/EBP) bind to overlapping elements within the interleukin-8 promoter. The role of Oct-1 as a transcriptional repressor. J Biol Chem 272(4):2396-2403
103. Riveros C, Mellor D, Gandhi KS, McKay FC, Cox MB, Berretta R, Vaezpour SY, Inostroza-Ponta M, Broadley SA, Heard RN, Vucic S, Stewart GJ, Williams DW, Scott RJ, Lechner-Scott J, Booth DR, Moscato P, ANZ gene Multiple Sclerosis Genetics Consortium, (2010) A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis. PLoS One 5(12):e14176
104. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets - 10 years on. Nucleic Acids Res 39(Database issue):D1005-D1010
105. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38(Database issue):D355-D360
106. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25-29
107. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG (2009) DIANA-mirPath: integrating human and mouse microRNAs in pathways. Bioinformatics 25(15):1991-1993
108. Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP (2009) MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 37(Web Server issue):W356-W362
109. Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23(2):257-258
110. Johnson GL, Lapadat R (2002) Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases. Science 298(5600):1911-1912
111. Ferrandi C, Richard F, Tavano P, Hauben E, Barbié V, Gotteland JP, Greco B, Fortunato M, Mariani MF, Furlan R, Comi G, Martino G, Zaratin PF (2011) Characterization of immune cell subsets during the active phase of multiple sclerosis reveals disease and c-Jun N-terminal kinase pathway biomarkers. Mult Scler 17(1):43-56
112. Noubade R, Krementsov DN, Del Rio R, Thornton T, Nagaleekar V, Saligrama N, Spitzack A, Spach K, Sabio G, Davis RJ, Rincon M, Teuscher C (2011) Activation of p38 MAPK in CD4 T cells controls IL-17 production and autoimmune encephalomyelitis. Blood 118(12):3290-3300
113. Tran EH, Azuma YT, Chen M, Weston C, Davis RJ, Flavell RA (2006) Inactivation of JNK1 enhances innate IL-10 production and dampens autoimmune inflammation in the brain. Proc Natl Acad Sci U S A 103(36):13451-13456
114. Bettelli E, Carrier Y, Gao W, Korn T, Strom TB, Oukka M, Weiner HL, Kuchroo VK (2006) Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells. Nature 441(7090):235-238
115. Veldhoen M, Hocking RJ, Atkins CJ, Locksley RM, Stockinger B (2006) TGFbeta in the context of an inflammatory cytokine milieu supports de novo differentiation of IL-17-producing T cells. Immunity 24(2):179-189
116. Meoli EM, Oh U, Grant CW, Jacobson S (2011) TGF-beta signaling is altered in the peripheral blood of subjects with multiple sclerosis. J Neuroimmunol 230(1-2):164-168
117. Wang HH, Dai YQ, Qiu W, Lu ZQ, Peng FH, Wang YG, Bao J, Li Y, Hu XQ (2011) Interleukin-17-secreting T cells in neuromyelitis optica and multiple sclerosis during relapse. J Clin Neurosci 18(10):1313-1317
118. Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39(Database issue):D202-D209
119. Nikitin A, Egorov S, Daraselia N, Mazo I (2003) Pathway studio - the analysis and navigation of molecular networks. Bioinformatics 19(16):2155-2157
120. Junker A, Krumbholz M, Eisele S, Mohan H, Augstein F, Bittner R, Lassmann H, Wekerle H, Hohlfeld R, Meinl E (2009) Micro-RNA profiling of multiple sclerosis lesions identifies modulators of the regulatory protein CD47. Brain 132(Pt 12):3342-3352
121. Soreq H, Wolf Y (2011) NeurimmiRs: microRNAs in the neuroimmune interface. Trends Mol Med 17(10):548-555
122. Tu K, Yu H, Hua YJ, Li YY, Liu L, Xie L, Li YX (2009) Combinatorial network of primary and secondary microRNAdriven regulatory mechanisms. Nucleic Acids Res 37(18):5969-5980
123. Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466(7308):835-840
124. Cortez MA, Calin GA (2009) MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases. Expert Opin Biol Ther 9(6):703-711
125. Théry C, Ostrowski M, Segura E (2009) Membrane vesicles as conveyors of immune responses. Nat Rev Immunol 9(8):581-593
126. Valadi H, Ekström K, Bossios A, Sjöstrand M, Lee JJ, Lötvall JO (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9(6):654-659
127. Wyman SK, Knouf EC, Parkin RK, Fritz BR, Lin DW, Dennis LM, KrouseMA,Webster PJ, TewariM(2011) Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res 21 (9):1450-1461