Disease Embryo Development Network Reveals the Relationship Between Disease Genes and Embryo Development Genes

Overview

Journal J Theor Biol

Publisher Elsevier

Specialty Biology

Date 2011 Aug 10

PMID 21824480

Citations 2

Authors

Binsheng Gong

Tao Liu

Xiaoyu Zhang

Xi Chen

Jiang Li

Hongchao Lv

Yi Zou

Xia Li

Shaoqi Rao

Affiliations

Soon will be listed here.

Abstract

A basic problem for contemporary biology and medicine is exploring the correlation between human disease and underlying cellular mechanisms. For a long time, several efforts were made to reveal the similarity between embryo development and disease process, but few from the system level. In this article, we used the human protein-protein interactions (PPIs), disease genes with their classifications and embryo development genes and reconstructed a human disease-embryo development network to investigate the relationship between disease genes and embryo development genes. We found that disease genes and embryo development genes are prone to connect with each other. Furthermore, diseases can be categorized into three groups according to the closeness with embryo development in gene overlapping, interacting pattern in PPI network and co-regulated by microRNAs or transcription factors. Embryo development high-related disease genes show their closeness with embryo development at least in three biological levels. But it is not for embryo development medium-related disease genes and embryo development low-related disease genes. We also found that embryo development high-related disease genes are more central than other disease genes in the human PPI network. In addition, the results show that embryo development high-related disease genes tend to be essential genes compared with other diseases' genes. This network-based approach could provide evidence for the intricate correlation between disease process and embryo development, and help to uncover potential mechanisms of human complex diseases.

Citing Articles

Editorial: Advances in genomic and genetic tools, and their applications for understanding embryonic development and human diseases.

Abu-Elmagd M, Assidi M, Alrefaei A, Rebai A Front Cell Dev Biol. 2022; 10:1016400.

PMID: 36478744 PMC: 9720382. DOI: 10.3389/fcell.2022.1016400.

Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues.

Xu J, Feng L, Han Z, Li Y, Wu A, Shao T Nucleic Acids Res. 2016; 44(19):9438-9451.

PMID: 27365046 PMC: 5100587. DOI: 10.1093/nar/gkw587.

References

Chou K, Forsen S . Graphical rules for enzyme-catalysed rate laws. Biochem J. 1980; 187(3):829-35. PMC: 1162468. DOI: 10.1042/bj1870829. View

Sinclair K, Singh R . Modelling the developmental origins of health and disease in the early embryo. Theriogenology. 2006; 67(1):43-53. DOI: 10.1016/j.theriogenology.2006.09.017. View

Chou K . Two new schematic rules for rate laws of enzyme-catalysed reactions. J Theor Biol. 1981; 89(4):581-92. DOI: 10.1016/0022-5193(81)90030-8. View

Althaus I, Gonzales A, Chou J, Romero D, Deibel M, Chou K . The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J Biol Chem. 1993; 268(20):14875-80. View

Lee D, Park J, Kay K, Christakis N, Oltvai Z, Barabasi A . The implications of human metabolic network topology for disease comorbidity. Proc Natl Acad Sci U S A. 2008; 105(29):9880-5. PMC: 2481357. DOI: 10.1073/pnas.0802208105. View

Merrick D, Stadler L, Larner D, Smith J . Muscular dystrophy begins early in embryonic development deriving from stem cell loss and disrupted skeletal muscle formation. Dis Model Mech. 2009; 2(7-8):374-88. PMC: 2707105. DOI: 10.1242/dmm.001008. View

Cusick M, Klitgord N, Vidal M, Hill D . Interactome: gateway into systems biology. Hum Mol Genet. 2005; 14 Spec No. 2:R171-81. DOI: 10.1093/hmg/ddi335. View

Yu J, Sun X, Wang J . TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J Theor Biol. 2009; 261(3):459-68. PMC: 7094124. DOI: 10.1016/j.jtbi.2009.08.005. View

Friedman A, Perrimon N . Genetic screening for signal transduction in the era of network biology. Cell. 2007; 128(2):225-31. DOI: 10.1016/j.cell.2007.01.007. View

10.

Chou K . Some remarks on protein attribute prediction and pseudo amino acid composition. J Theor Biol. 2010; 273(1):236-47. PMC: 7125570. DOI: 10.1016/j.jtbi.2010.12.024. View

11.

Ergun A, Lawrence C, Kohanski M, Brennan T, Collins J . A network biology approach to prostate cancer. Mol Syst Biol. 2007; 3:82. PMC: 1828752. DOI: 10.1038/msb4100125. View

12.

Postovit L, Margaryan N, Seftor E, Kirschmann D, Lipavsky A, Wheaton W . Human embryonic stem cell microenvironment suppresses the tumorigenic phenotype of aggressive cancer cells. Proc Natl Acad Sci U S A. 2008; 105(11):4329-34. PMC: 2393795. DOI: 10.1073/pnas.0800467105. View

13.

Gonzalez-Diaz H, Perez-Montoto L, Duardo-Sanchez A, Paniagua E, Vazquez-Prieto S, Vilas R . Generalized lattice graphs for 2D-visualization of biological information. J Theor Biol. 2009; 261(1):136-47. PMC: 7094121. DOI: 10.1016/j.jtbi.2009.07.029. View

14.

Giallourakis C, Henson C, Reich M, Xie X, Mootha V . Disease gene discovery through integrative genomics. Annu Rev Genomics Hum Genet. 2005; 6:381-406. DOI: 10.1146/annurev.genom.6.080604.162234. View

15.

Lalli E, Alonso J . Targeting DAX-1 in embryonic stem cells and cancer. Expert Opin Ther Targets. 2010; 14(2):169-77. DOI: 10.1517/14728220903531454. View

16.

Giuffrida D, Rogers I, Nagy A, Calogero A, Brown T, Casper R . Human embryonic stem cells secrete soluble factors that inhibit cancer cell growth. Cell Prolif. 2009; 42(6):788-98. PMC: 6495992. DOI: 10.1111/j.1365-2184.2009.00640.x. View

17.

Zhu X, Gerstein M, Snyder M . Getting connected: analysis and principles of biological networks. Genes Dev. 2007; 21(9):1010-24. DOI: 10.1101/gad.1528707. View

18.

Zhou G, Deng M . An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. Biochem J. 1984; 222(1):169-76. PMC: 1144157. DOI: 10.1042/bj2220169. View

19.

Monzo M, Navarro A, Bandres E, Artells R, Moreno I, Gel B . Overlapping expression of microRNAs in human embryonic colon and colorectal cancer. Cell Res. 2008; 18(8):823-33. DOI: 10.1038/cr.2008.81. View

20.

Ma Y, Zhang P, Wang F, Moyer M, Yang J, Liu Z . Human embryonic stem cells and metastatic colorectal cancer cells shared the common endogenous human microRNA-26b. J Cell Mol Med. 2010; 15(9):1941-54. PMC: 3918049. DOI: 10.1111/j.1582-4934.2010.01170.x. View