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

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

Research output: Contribution to journalArticle

13 Citations (Scopus)

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 - 2013
Externally publishedYes

Fingerprint

Long Noncoding RNA
Fractals
Alzheimer's Disease
Fractal dimension
Bioinformatics
Computational Biology
Fractal Dimension
DNA sequences
Messenger RNA
Alzheimer Disease
Drugs
DNA Sequence
Coding
Pharmaceutical Preparations
Higher Dimensions
RNA
Genes
Gene
Glycoproteins
Glycoprotein

ASJC Scopus subject areas

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

Cite this

Exploratory bioinformatics study of lncRNAs in Alzheimer's disease mRNA sequences with application to drug development. / Holden, T.; Nguyen, A.; Lin, Elaine; Cheung, E.; Dehipawala, S.; Ye, J.; Tremberger, G.; Lieberman, D.; Cheung, T.

In: Computational and Mathematical Methods in Medicine, Vol. 2013, 579136, 2013.

Research output: Contribution to journalArticle

Holden, T. ; Nguyen, A. ; Lin, Elaine ; Cheung, E. ; Dehipawala, S. ; Ye, J. ; Tremberger, G. ; Lieberman, D. ; Cheung, T. / Exploratory bioinformatics study of lncRNAs in Alzheimer's disease mRNA sequences with application to drug development. In: Computational and Mathematical Methods in Medicine. 2013 ; Vol. 2013.
@article{045907099480408bba6c03f8db40ac9a,
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.",
author = "T. Holden and A. Nguyen and Elaine Lin and E. Cheung and S. Dehipawala and J. Ye and G. Tremberger and D. Lieberman and T. Cheung",
year = "2013",
doi = "10.1155/2013/579136",
language = "English (US)",
volume = "2013",
journal = "Computational and Mathematical Methods in Medicine",
issn = "1748-670X",
publisher = "Hindawi Publishing Corporation",

}

TY - JOUR

T1 - Exploratory bioinformatics study of lncRNAs in Alzheimer's disease mRNA sequences with application to drug development

AU - Holden, T.

AU - Nguyen, A.

AU - Lin, Elaine

AU - Cheung, E.

AU - Dehipawala, S.

AU - Ye, J.

AU - Tremberger, G.

AU - Lieberman, D.

AU - Cheung, T.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84877267531&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84877267531&partnerID=8YFLogxK

U2 - 10.1155/2013/579136

DO - 10.1155/2013/579136

M3 - Article

C2 - 23662159

AN - SCOPUS:84877267531

VL - 2013

JO - Computational and Mathematical Methods in Medicine

JF - Computational and Mathematical Methods in Medicine

SN - 1748-670X

M1 - 579136

ER -