Identifying differentially expressed genes in DNA microarray data

2021 ◽  
Author(s):  
Lit-Hsin Loo
Keyword(s):  
Differentially Expressed Genes ◽  
Dna Microarray ◽  
Microarray Data ◽  
Differentially Expressed ◽  
Dna Microarray Data

scholarly journals Comparative functional genomic analysis of Alzheimer’s affected and naturally aging brains

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8682
Author(s):  
Yi-Shian Peng ◽  
Chia-Wei Tang ◽  
Yi-Yun Peng ◽  
Hung Chang ◽  
Chien-Lung Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Microarray Data ◽  
Gene List ◽  
Amyloid Β ◽  
Differentially Expressed ◽  
Gene Expression Microarray ◽  
Expression Microarray ◽  
Functional Genomic Analysis ◽  
Gene Expression Microarray Data

Background Alzheimer’s disease (AD) is a prevalent progressive neurodegenerative human disease whose cause remains unclear. Numerous initially highly hopeful anti-AD drugs based on the amyloid-β (Aβ) hypothesis of AD have failed recent late-phase tests. Natural aging (AG) is a high-risk factor for AD. Here, we aim to gain insights in AD that may lead to its novel therapeutic treatment through conducting meta-analyses of gene expression microarray data from AG and AD-affected brain. Methods Five sets of gene expression microarray data from different regions of AD (hereafter, ALZ when referring to data)-affected brain, and one set from AG, were analyzed by means of the application of the methods of differentially expressed genes and differentially co-expressed gene pairs for the identification of putatively disrupted biological pathways and associated abnormal molecular contents. Results Brain-region specificity among ALZ cases and AG-ALZ differences in gene expression and in KEGG pathway disruption were identified. Strong heterogeneity in AD signatures among the five brain regions was observed: HC/PC/SFG showed clear and pronounced AD signatures, MTG moderately so, and EC showed essentially none. There were stark differences between ALZ and AG. OXPHOS and Proteasome were the most disrupted pathways in HC/PC/SFG, while AG showed no OXPHOS disruption and relatively weak Proteasome disruption in AG. Metabolic related pathways including TCA cycle and Pyruvate metabolism were disrupted in ALZ but not in AG. Three pathogenic infection related pathways were disrupted in ALZ. Many cancer and signaling related pathways were shown to be disrupted AG but far less so in ALZ, and not at all in HC. We identified 54 “ALZ-only” differentially expressed genes, all down-regulated and which, when used to augment the gene list of the KEGG AD pathway, made it significantly more AD-specific.

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