An Information-theoretical Analysis of Gene Nucleotide Sequence Structuredness for a Selection of Aging and Cancer-related Genes

Overview

Journal Genomics Inform

Publisher Biomed Central

Specialty Biology

Date 2021 Jan 8

PMID 33412757

Authors

David Blokh

Joseph Gitarts

Ilia Stambler

Affiliations

Soon will be listed here.

Abstract

We provide an algorithm for the construction and analysis of autocorrelation (information) functions of gene nucleotide sequences. As a measure of correlation between discrete random variables, we use normalized mutual information. The information functions are indicative of the degree of structuredness of gene sequences. We construct the information functions for selected gene sequences. We find a significant difference between information functions of genes of different types. We hypothesize that the features of information functions of gene nucleotide sequences are related to phenotypes of these genes.

References

Blokh D, Stambler I . The application of information theory for the research of aging and aging-related diseases. Prog Neurobiol. 2016; 157:158-173. DOI: 10.1016/j.pneurobio.2016.03.005. View

Shimizu Y, Luk H, Horio D, Miron P, Griswold M, Iglehart D . BRCA1-IRIS overexpression promotes formation of aggressive breast cancers. PLoS One. 2012; 7(4):e34102. PMC: 3325250. DOI: 10.1371/journal.pone.0034102. View

Song L, Langfelder P, Horvath S . Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics. 2012; 13:328. PMC: 3586947. DOI: 10.1186/1471-2105-13-328. View

Ran L, Chen Y, Zhang Z, Tao N, Ren J, Zhou L . SIRT6 Overexpression Potentiates Apoptosis Evasion in Hepatocellular Carcinoma via BCL2-Associated X Protein-Dependent Apoptotic Pathway. Clin Cancer Res. 2016; 22(13):3372-82. DOI: 10.1158/1078-0432.CCR-15-1638. View

Bosch-Presegue L, Vaquero A . The dual role of sirtuins in cancer. Genes Cancer. 2011; 2(6):648-62. PMC: 3174263. DOI: 10.1177/1947601911417862. View

Androulakis I, Yang E, Almon R . Analysis of time-series gene expression data: methods, challenges, and opportunities. Annu Rev Biomed Eng. 2007; 9:205-28. PMC: 4181347. DOI: 10.1146/annurev.bioeng.9.060906.151904. View

Blokh D, Stambler I, Lubart E, Mizrahi E . An Information Theory Approach for the Analysis of Individual and Combined Evaluation Parameters of Multiple Age-Related Diseases. Entropy (Basel). 2020; 21(6). PMC: 7515061. DOI: 10.3390/e21060572. View

Shan Y, Hsu H, Lai M, Hung Y, Wang C, Yen M . Cyclin D1 overexpression correlates with poor tumor differentiation and prognosis in gastric cancer. Oncol Lett. 2017; 14(4):4517-4526. PMC: 5594254. DOI: 10.3892/ol.2017.6736. View

James B, Luczak B, Girgis H . MeShClust: an intelligent tool for clustering DNA sequences. Nucleic Acids Res. 2018; 46(14):e83. PMC: 6101578. DOI: 10.1093/nar/gky315. View

10.

Blokh D, Zurgil N, Stambler I, Afrimzon E, Shafran Y, Korech E . An information-theoretical model for breast cancer detection. Methods Inf Med. 2008; 47(4):322-7. View

11.

Roy R, Chun J, Powell S . BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nat Rev Cancer. 2011; 12(1):68-78. PMC: 4972490. DOI: 10.1038/nrc3181. View

12.

Blokh D, Stambler I, Afrimzon E, Platkov M, Shafran Y, Korech E . Comparative analysis of cell parameter groups for breast cancer detection. Comput Methods Programs Biomed. 2009; 94(3):239-49. DOI: 10.1016/j.cmpb.2009.01.005. View

13.

Saha S, Mandal P, Ganguly S, Jana D, Ayaz A, Banerjee A . Decreased Expression of BRCA2 Accelerates Sporadic Breast Cancer Progression. Indian J Surg Oncol. 2016; 6(4):378-383. PMC: 4809839. DOI: 10.1007/s13193-015-0449-1. View

14.

Jin X, Wei Y, Xu F, Zhao M, Dai K, Shen R . SIRT1 promotes formation of breast cancer through modulating Akt activity. J Cancer. 2018; 9(11):2012-2023. PMC: 5995935. DOI: 10.7150/jca.24275. View

15.

Vinga S . Information theory applications for biological sequence analysis. Brief Bioinform. 2013; 15(3):376-89. PMC: 7109941. DOI: 10.1093/bib/bbt068. View

16.

Romagosa C, Simonetti S, Lopez-Vicente L, Mazo A, LLeonart M, Castellvi J . p16(Ink4a) overexpression in cancer: a tumor suppressor gene associated with senescence and high-grade tumors. Oncogene. 2011; 30(18):2087-97. DOI: 10.1038/onc.2010.614. View

17.

Singh P, Demmitt B, Nath R, Brunet A . The Genetics of Aging: A Vertebrate Perspective. Cell. 2019; 177(1):200-220. PMC: 7592626. DOI: 10.1016/j.cell.2019.02.038. View

18.

Joosse S . BRCA1 and BRCA2: a common pathway of genome protection but different breast cancer subtypes. Nat Rev Cancer. 2012; 12(5):372. DOI: 10.1038/nrc3181-c2. View

19.

Blokh D, Stambler I, Afrimzon E, Shafran Y, Korech E, Sandbank J . The information-theory analysis of Michaelis-Menten constants for detection of breast cancer. Cancer Detect Prev. 2007; 31(6):489-98. DOI: 10.1016/j.cdp.2007.10.010. View

20.

Priness I, Maimon O, Ben-Gal I . Evaluation of gene-expression clustering via mutual information distance measure. BMC Bioinformatics. 2007; 8:111. PMC: 1858704. DOI: 10.1186/1471-2105-8-111. View