RESUMO
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.
RESUMO
Cluster analysis of DNA microarray data that uses statistical algorithms to arrange the genes according to similarity in patterns of gene expression and the output displayed graphically is described in this article. Hierarchical clustering is a multivariate tool often used in phylogenetics, comparative genomics to relate the evolution of species. The patterns seen in microarray expression data can be interpreted as indications of the status of the genes responsible for nephropathy in peripheral blow cells of type 2 diabetes (T2DN). Out of 415 genes totally expressed in the 3 DNA chips it was concluded that only 116 genes expressed in T2DN and in that only 50 are functional genes. These 50 functional genes are responsible for diabetic nephropathy; of these 50, some of the genes which are more expressed and responsible are AGXT: Alanine-glyoxylate aminotransferase, RHOD: Ras homolog gene family, CAPN6: Calpain 6, EFNB2: Ephrin-B2, ANXA7: Annexin A7, PEG10: Paternally expressed 10, DPP4: Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2), ENSA: Endosulfine alpha, IGFBP2: Insulin-like growth factor binding protein 2, 36kDa, CENPB: Centromere protein B, 80kDa, MLL3: Myeloid/lymphoid or mixed-lineage leukemia 3, BDNF: Brain-derived neurotrophic factor, EIF4A2: Eukaryotic translation initiation factor 4A, isoform 2, PPP2R1A: Protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform. Fifty genes and their nucleotide sequences are taken from NCBI and a phylogenetic tree is constructed using CLUSTAL W and the distances are closer to each other concluding that based on the sequence similarity and evolution the genes are expressed similarly. Literature survey is done for each gene in OMIM and the genes responsible for diabetic nephropathy are listed.
