Studying the differential co-expression of microRNAs reveals significant role of white matter in early Alzheimer's progression

Molecular BioSystems

Volumn 9, Issue 3, 2013, Pages 457-466

  Bhattacharyya, Malay ^a   Bandyopadhyay, Sanghamitra ^a  

^a INDIAN STATISTICAL INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MIRN423 MICRORNA, HUMAN; TRANSCRIPTOME;

ALGORITHM; ALZHEIMER DISEASE; ARTICLE; BIOLOGICAL MODEL; BRAIN CORTEX; COMPARATIVE STUDY; DISEASE COURSE; FEMALE; GENE REGULATORY NETWORK; GENETICS; HUMAN; METABOLISM; PATHOLOGY; PHENOTYPE; VERY ELDERLY;

AGED, 80 AND OVER; ALGORITHMS; ALZHEIMER DISEASE; CEREBRAL CORTEX; DISEASE PROGRESSION; FEMALE; GENE REGULATORY NETWORKS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MICRORNAS; MODELS, BIOLOGICAL; PHENOTYPE; TRANSCRIPTOME;

MLCS; MLOWN;

EID: 84875834246     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c2mb25434d     Document Type: Article

References (35)

1. D. P. Bartel MicroRNAs: target recognition and regulatory functions Cell 2009 136 2 215 233
2. N. N. Hooten K. Abdelmohsen M. Gorospe N. Ejiogu A. B. Zonderman M. K. Evans MicroRNA expression patterns reveal differential expression of target genes with age PLoS One 2010 5 5 e10724
3. W. X. Wang B. W. Rajeev A. J. Stromberg N. Ren G. Tang Q. Huang I. Rigoutsos P. T. Nelson The expression of microRNA miR-107 decreases early in alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1 J. Neurosci. 2008 28 5 1213 1223
4. N. Schonrock Y. D. Ke D. Humphreys M. Staufenbiel L. M. Ittner T. Preiss J. Götz Neuronal microRNA deregulation in response to Alzheimer's disease amyloid-β PLoS One 2010 5 6 e11070
5. V. G. Tusher R. Tibshirani G. Chu Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. U. S. A. 2001 98 9 5116 5121
6. N. Filigheddu I. Gregnanin P. E. Porporato D. Surico B. Perego L. Galli C. Patrignani A. Graziani N. Surico Differential expression of microRNAs between eutopic and ectopic endometrium in ovarian endometriosis J. Biomed. Biotechnol. 2010 369 549
7. Z. G. Mao D. S. He J. Zhou B. Yao W. W. Xiao C. H. Chen Y. H. Zhu H. J. Wang Differential expression of microRNAs in GH-secreting pituitary adenomas Diagn. Pathol. 2010 5 1 79
8. S. Ura M. Honda T. Yamashita T. Ueda H. Takatori R. Nishino H. Sunakozaka Y. Sakai K. Horimoto S. Kaneko Differential microRNA expression between hepatitis B and hepatitis C leading disease progression to hepatocellular carcinoma Hepatology 2009 49 4 1098 1112
9. C. F. Stählera A. Kellera P. Leidingerb C. Backesb A. Chandranc J. Wischhusenc B. Meder E. Meese Whole mirnome-wide differential co-expression of microRNAs Genomics, Proteomics Bioinf. 2012 10 5 285 294
10. M. C. Oldham S. Horvath D. H. Geschwind Conservation and evolution of gene coexpression networks in human and chimpanzee brains Proc. Natl. Acad. Sci. U. S. A. 2006 103 47 17973 17978
11. K. Duff F. Suleman Transgenic mouse models of alzheimer's disease: How useful have they been for therapeutic development? Briefings Funct. Genomics Proteomics 2004 3 1 47 59
12. J. A. Saugstad MicroRNAs as effectors of brain function with roles in ischemia and injury, neuroprotection, and neurodegeneration J. Cereb. Blood Flow Metab. 2010 30 9 1564 1576
13. M. A. Christensen W. Zhou H. Qing A. Lehman S. Philipsen W. Song Transcriptional regulation of BACE1, the beta-amyloid precursor protein beta-secretase Mol. Cell. Biol. 2003 24 2 865 874
14. J. Satoh MicroRNAs and their therapeutic potential for human diseases: Aberrant microRNA expression in Alzheimer's disease brains J. Pharmacol. Sci. 2010 114 3 269 275
15. W. X. Wang Q. Huang Y. Hu A. J. Stromberg P. T. Nelson Patterns of microRNA expression in normal and early Alzheimer's disease human temporal cortex: white matter versus gray matter Acta Neuropathol. 2010 121 2 193 205
16. L. M. Ittner N. Schonrock M. Matamales J. Götz MicroRNA networks surrounding APP and amyloid-β metabolism-implications for alzheimer's disease Exp. Neurol. 2012 235 2 447 454
17. J. Y. Yu K. H. Chung M. Deo R. C. Thompson D. L. Turner MicroRNA miR-124 regulates neurite outgrowth during neuronal differentiation Exp. Cell Res. 2008 314 14 2618 2633
18. R. B. Campenot Local control of neurite development by nerve growth factor Proc. Natl. Acad. Sci. U. S. A. 1977 74 10 4516 4519
19. J. K. Choi U. Yu O. J. Yoo S. Kim Differential coexpression analysis using microarray data and its application to human cancer Bioinformatics 2005 21 24 4348 4355
20. M. Watson Coxpress: differential co-expression in gene expression data BMC Bioinformatics 2006 7 509
21. J. Gillis P. Pavlidis A methodology for the analysis of differential coexpression across the human lifespan BMC Bioinformatics 2009 10 306
22. Y. Choi C. Kendziorski Statistical methods for gene set co-expression analysis Bioinformatics 2009 25 21 2780 2786
23. G. Fang, R. Kuang, G. Pandey, M. Steinbach, C. L. Myers and V. Kumar, Subspace differential coexpression analysis: Problem definition and a general approach, in Proceedings of the Pacific Symposium on Biocomputing, 2010, vol. 15, pp. 145-156
24. T. Idekera N. J. Krogan Differential network biology Mol. Syst. Biol. 2012 8 565
25. S. Bandyopadhyay M. Bhattacharyya A biologically inspired measure for co-expression analysis IEEE/ACM Trans. Comput. Biol. Bioinf. 2011 8 4 929 942
26. P. Alexiou T. Vergoulis M. Gleditzsch G. Prekas T. Dalamagas M. Megraw I. Grosse T. Sellis A. G. Hatzigeorgiou miRGen 2.0: a database of microRNA genomic information and regulation Nucleic Acids Res. 2009 38 D137 D141
27. J. Wang M. Lu C. Qiu Q. Cui TransmiR: a transcription factor-microRNA regulation database Nucleic Acids Res. 2009 38 D119 D122
28. Y. Matsunoshita K. Ijiri Y. Ishidou S. Nagano T. Yamamoto H. Nagao S. Komiya T. Setoguchi Suppression of osteosarcoma cell invasion by chemotherapy is mediated by urokinase plasminogen activator activity via up-regulation of EGR1 PLoS One 2011 6 1 e16234
29. P. Renbaum R. Beeri E. Gabai M. Amiel M. Gal M. U. Ehrengruber E. Levy-Lahad Egr-1 upregulates the Alzheimer's disease presenilin-2 gene in neuronal cells Gene 2003 318 113 124
30. A. Giovanni E. Keramaris E. J. Morris S. T. Hou M. O'Hare N. Dyson G. S. Robertson R. S. Slack D. S. Park E2F1 mediates death of B-amyloid-treated cortical neurons in a manner independent of p53 and dependent on Bax and Caspase 3 J. Biol. Chem. 2000 275 11553 11560
31. J. Rhodes K. Jordan-Sciutto R. Bowser Altered subcellular distribution of transcriptional regulators in response to Aβ peptide and during Alzheimer's disease Mech. Ageing Dev. 2001 123 1 11 20
32. B. Pakkenberg H. J. G. Gundersen Neocortical neuron number in humans: effect of sex and age J. Comp. Neurol. 1997 384 312 320
33. A. E. Roher N. Weiss T. A. Kokjohn Y. Kuo W. Kalback J. Anthony D. Watson D. C. Luehrs L. Sue D. Walker M. Emmerling W. Goux T. Beach Increased Aβ peptides and reduced cholesterol and myelin proteins characterize white matter degeneration in alzheimer's disease Biochemistry 2002 41 37 11080 11090
34. B. T. Gold D. K. Powell A. H. Andersen C. D. Smith Alterations in multiple measures of white matter integrity in normal women at high risk for alzheimer's disease NeuroImage 2010 52 4 1487 1494
35. F.-E. de Leeuw F. Barkhof P. Scheltens Progression of cerebral white matter lesions in Alzheimer's disease: a new window for therapy? J. Neurol. Neurosurg. Psychiatry 2005 76 9 1286 1288