Exploratory bioinformatics study of lncRNAs in Alzheimer's disease mRNA sequences with application to drug development

T. Holden, A. Nguyen, E. Lin, E. Cheung, S. Dehipawala, J. Ye, G. Tremberger, D. Lieberman, T. Cheung

Research output: Contribution to journalArticle

13 Scopus citations

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.

Original languageEnglish (US)
Article number579136
JournalComputational and Mathematical Methods in Medicine
Volume2013
DOIs
StatePublished - May 13 2013

ASJC Scopus subject areas

  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Applied Mathematics

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    Holden, T., Nguyen, A., Lin, E., Cheung, E., Dehipawala, S., Ye, J., Tremberger, G., Lieberman, D., & Cheung, T. (2013). Exploratory bioinformatics study of lncRNAs in Alzheimer's disease mRNA sequences with application to drug development. Computational and Mathematical Methods in Medicine, 2013, [579136]. https://doi.org/10.1155/2013/579136