title: Exploratory bioinformatics study of lncRNAs in Alzheimer's disease mRNA sequences with application to drug development.
abstract: Long noncoding RNA (lncRNA) within mRNA sequences of Alzheimer's disease genes, namely, APP, APOE, PSEN1, and PSEN2, has been analyzed using fractal dimension (FD) computation and correlation analysis. We examined lncRNA by comparing mRNA FD to corresponding coding DNA sequences (CDSs) FD. APP, APOE, and PSEN1 CDSs select slightly higher FDs compared to the mRNA, while PSEN2 CDSs FDs are lower. The correlation coefficient for these sequences is 0.969. A comparative study of differentially expressed MAPK signaling pathway lncRNAs in pancreatic cancer cells shows a correlation of 0.771. Selection of higher FD CDSs could indicate interaction of Alzheimer's gene products APP, APOE, and PSEN1. Including hypocretin sequences (where all CDSs have higher fractal dimensions than mRNA) in the APP, APOE, and PSEN1 sequence analyses improves correlation, but the inclusion of erythropoietin (where all CDSs have higher FD than mRNA) would suppress correlation, suggesting that HCRT, a hypothalamus neurotransmitter related to the wake/sleep cycle, might be better when compared to EPO, a glycoprotein hormone, for targeting Alzheimer's disease drug development. Fractal dimension and entropy correlation have provided supporting evidence, consistent with evolutionary studies, for using a zebrafish model together with a mouse model, in HCRT drug development.
authors: Queensborough Community College of CUNY, 222-05 56th Avenue Bayside, NY 11364, USA.
authors: T
authors: T
authors: Holden
authors: A
authors: A
authors: Nguyen
authors: E
authors: E
authors: Lin
authors: E
authors: E
authors: Cheung
authors: S
authors: S
authors: Dehipawala
authors: J
authors: J
authors: Ye
authors: G
authors: G
authors: Tremberger
authors: D
authors: D
authors: Lieberman
authors: T
authors: T
authors: Cheung
mesh_terms: D015720:5'-Nucleotidase / Q000235:genetics; D000544:Alzheimer Disease / Q000188:drug therapy / Q000235:genetics*; D016564:Amyloid beta-Protein Precursor / Q000235:genetics; D000818:Animals; D001057:Apolipoproteins E / Q000235:genetics; D019295:Computational Biology; D004195:Disease Models, Animal; D055808:Drug Discovery; D004921:Erythropoietin / Q000235:genetics; D017709:Fractals; D006023:Glycoproteins / Q000235:genetics; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D051379:Mice; D009479:Neuropeptides / Q000235:genetics; D064446:Orexin Receptors / Q000235:genetics; D000068797:Orexins; D053766:Presenilin-2 / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D017467:Receptors, Erythropoietin / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000706:statistics & numerical data; D015027:Zebrafish
chemical_list: D016564:Amyloid beta-Protein Precursor; D001057:Apolipoproteins E; C554270:EPO protein, human; D006023:Glycoproteins; D047908:Intracellular Signaling Peptides and Proteins; D009479:Neuropeptides; D064446:Orexin Receptors; D000068797:Orexins; C508861:PSEN2 protein, human; D053766:Presenilin-2; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D017467:Receptors, Erythropoietin; D004921:Erythropoietin; D015720:5'-Nucleotidase; C412794:NT5C3A protein, human
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