Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development

Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development

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,...

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Main Authors: Holden, T., Nguyen, A., Lin, E., Cheung, E., Dehipawala, S., Ye, J., Tremberger, G., Lieberman, D., Cheung, T.
Format: Online
Language:English
Published: Hindawi Publishing Corporation 2013
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639631/
id pubmed-3639631
recordtype oai_dc
spelling pubmed-36396312013-05-09 Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development Holden, T. Nguyen, A. Lin, E. Cheung, E. Dehipawala, S. Ye, J. Tremberger, G. Lieberman, D. Cheung, T. Research Article 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. Hindawi Publishing Corporation 2013 2013-04-11 /pmc/articles/PMC3639631/ /pubmed/23662159 http://dx.doi.org/10.1155/2013/579136 Text en Copyright © 2013 T. Holden et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Holden, T.
Nguyen, A.
Lin, E.
Cheung, E.
Dehipawala, S.
Ye, J.
Tremberger, G.
Lieberman, D.
Cheung, T.
spellingShingle Holden, T.
Nguyen, A.
Lin, E.
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
author_facet Holden, T.
Nguyen, A.
Lin, E.
Cheung, E.
Dehipawala, S.
Ye, J.
Tremberger, G.
Lieberman, D.
Cheung, T.
author_sort Holden, T.
title Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development
title_short Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development
title_full Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development
title_fullStr Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development
title_full_unstemmed Exploratory Bioinformatics Study of lncRNAs in Alzheimer's Disease mRNA Sequences with Application to Drug Development
title_sort exploratory bioinformatics study of lncrnas in alzheimer's disease mrna sequences with application to drug development
description 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.
publisher Hindawi Publishing Corporation
publishDate 2013
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639631/
_version_ 1611973710082736128

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