tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 06 2020
01 06 2020
Historique:
received:
02
07
2019
revised:
09
11
2019
accepted:
11
03
2020
pubmed:
15
3
2020
medline:
30
10
2020
entrez:
15
3
2020
Statut:
ppublish
Résumé
The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. mamkato@ncc.go.jp. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 32170925
pii: 5805387
doi: 10.1093/bioinformatics/btaa182
pmc: PMC7267821
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3597-3599Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
Références
Cell Syst. 2018 Mar 28;6(3):271-281.e7
pubmed: 29596782
Nature. 2015 Sep 10;525(7568):261-4
pubmed: 26308893
Cell. 2011 Mar 4;144(5):646-74
pubmed: 21376230
Biosystems. 2014 Jan;115:46-58
pubmed: 24262634
Nat Genet. 2018 Jun;50(6):895-903
pubmed: 29808029
Cancer Res. 2019 Mar 1;79(5):1010-1013
pubmed: 30563892
Nat Rev Cancer. 2015 Dec;15(12):730-45
pubmed: 26597528
Artif Life. 2006 Fall;12(4):617-34
pubmed: 16953788
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
Nature. 2014 Aug 14;512(7513):155-60
pubmed: 25079324
Cell. 2000 Jan 7;100(1):57-70
pubmed: 10647931
Cancer Res. 2013 Jan 1;73(1):41-9
pubmed: 23090114
R Soc Open Sci. 2017 Sep 27;4(9):171060
pubmed: 28989791
PLoS Comput Biol. 2006 Aug 18;2(8):e108
pubmed: 16933983
Nat Genet. 2015 Mar;47(3):209-16
pubmed: 25665006
Nature. 2010 Apr 15;464(7291):993-8
pubmed: 20393554
Syst Biol. 2015 Jan;64(1):e1-25
pubmed: 25293804
Math Biosci. 2011 Jan;229(1):22-9
pubmed: 21044636
Nucleic Acids Res. 2017 Jan 4;45(D1):D777-D783
pubmed: 27899578