Analyzing Microarray Data of Alzheimer's Using Cluster Analysis to Identify the Biomarker Genes

Alzheimer is characterized by the presence of senile plaques and neurofibrillary tangles in cortical regions of the brain. The experimental data is taken from Gene Expression Omnibus. A hierarchical Cluster analysis and TreeView were performed to group genes on the basis of the expression pattern. The dynamic change of expression over time and diverse patterns of expression support the concept of a complex local milieu. TreeView allows the organized data to be visualized. List of 24 genes were obtained which showed high expression levels. Three genes, SORL1, APP, and APOE, are suspected to cause Alzheimer's whereas the other 21 genes are related to other diseases but may also be found to be associated with Alzheimer's, and these are TMEM59, CCT4, IGF2R, SFPQ, PRDX3, RNF14, IDS, SSBP1, SYNE2, TXNL4A, STXBP3, SMARCB1, ULK2, AGTPBP1, FABP7, CALB1, H2AFY, COPA, SAP18, ATIC and SYNCRIP.

[1]  A. D. Roses,et al.  Association of apolipoprotein E allele €4 with late-onset familial and sporadic Alzheimer’s disease , 2006 .

[2]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[3]  R. Nitsch,et al.  The novel cytosolic RING finger protein dactylidin is up‐regulated in brains of patients with Alzheimer's disease , 2005, The European journal of neuroscience.

[4]  P. Martiat,et al.  Gene expression pattern of functional neuronal cells derived from human bone marrow mesenchymal stromal cells , 2008, BMC Genomics.

[5]  Hyoung-Gon Lee,et al.  Evidence of DNA damage in Alzheimer disease: phosphorylation of histone H2AX in astrocytes , 2008, AGE.

[6]  J. Morrison,et al.  Neocortical neuronal subpopulations labeled by a monoclonal antibody to calbindin exhibit differential vulnerability in Alzheimer's disease , 1991, Experimental Neurology.

[7]  A. Levey,et al.  Loss of apolipoprotein E receptor LR11 in Alzheimer disease. , 2004, Archives of neurology.

[8]  M. Leissring,et al.  Insulin-degrading enzyme is exported via an unconventional protein secretion pathway , 2009, Molecular Neurodegeneration.

[9]  A. Singleton,et al.  Genetic screening of Alzheimer's disease genes in Iberian and African samples yields novel mutations in presenilins and APP , 2010, Neurobiology of Aging.

[10]  J. Koenderink.  Q… , 2014, Les noms officiels des communes de Wallonie, de Bruxelles-Capitale et de la communaute germanophone.

[11]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[12]  Stuart Maudsley,et al.  Complex and Multidimensional Lipid Raft Alterations in a Murine Model of Alzheimer's Disease , 2010, International journal of Alzheimer's disease.

[13]  R. Gomis,et al.  Identification of iduronate-2-sulfatase in mouse pancreatic islets. , 2004, American journal of physiology. Endocrinology and metabolism.

[14]  M. Garcia-Blanco,et al.  Alternative splicing in disease and therapy , 2004, Nature Biotechnology.

[15]  T. Beißbarth,et al.  A Serial Analysis of Gene Expression Profile of the Alzheimer’s Disease Tg2576 Mouse Model , 2010, Neurotoxicity Research.

[16]  S. Oikawa,et al.  Mitochondrial peroxiredoxin‐3 protects hippocampal neurons from excitotoxic injury in vivo , 2003, Journal of neurochemistry.

[17]  F. Fahrenholz,et al.  Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice , 2009, BMC Genomics.

[18]  E. Kremmer,et al.  The Novel Membrane Protein TMEM59 Modulates Complex Glycosylation, Cell Surface Expression, and Secretion of the Amyloid Precursor Protein* , 2010, The Journal of Biological Chemistry.

[19]  S. M. de la Monte,et al.  Brain insulin-like growth factor and neurotrophin resistance in Parkinson's disease and dementia with Lewy bodies: potential role of manganese neurotoxicity. , 2009, Journal of Alzheimer's disease : JAD.

[20]  Ronald C. Petersen,et al.  Association of missense and 5′-splice-site mutations in tau with the inherited dementia FTDP-17 , 1998, Nature.

[21]  J. Rommens,et al.  Familial Alzheimer's disease in kindreds with missense mutations in a gene on chromosome 1 related to the Alzheimer's disease type 3 gene , 1995, Nature.

[22]  J. Nalbantoglu,et al.  Conspicuous accumulation of a single-stranded DNA binding protein in skeletal muscle fibers in inclusion body myositis. , 1994, The American journal of pathology.

[23]  M. Konsolaki,et al.  Identification of Novel Genes That Modify Phenotypes Induced by Alzheimer's β-Amyloid Overexpression in Drosophila , 2008, Genetics.

[24]  J. Pridgeon,et al.  A Method to Identify p62's UBA Domain Interacting Proteins , 2003, Biological Procedures Online.

[25]  M. Pericak-Vance,et al.  Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease , 1991, Nature.

[26]  Qingzhong Liu,et al.  Independent component analysis of Alzheimer's DNA microarray gene expression data , 2009, Molecular Neurodegeneration.

[27]  D. Pollen,et al.  Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease , 1995, Nature.