Supplementary (Model description, Parameter values, Model implementation,Experimental data analysis, Supporting Tables S1-S3 and Supporting Figures S1-S19) from Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation

This Supplementary file includes: (1) Model description, Parameter values, Model implementation, and Experimental data analysis. (2) Supporting Tables S1-S3. Table S1: The influence between gene mutation type and cell function; Table S2: Parameters used model simulation; and Table S3: Parameters for simplifying success DNA repair probability. (3) Supporting Figures S1-S19. Figure S1: Illustration of the model; Figure S2: The inflammatory score divided into mild, moderate, and severe; Figure S3: Illustration of the DNA damage/repair module; Figure S4: Cell fate decision after DNA damage; Figure S5: The functions for the probability of successful repair and the number of un-repaired damage locus obtained from stochastic simulation; Figure S6: Flow chart of the numerical scheme of the simulation process; Figure S7: Population dynamics with three stages; Figure S8: Major pathways responsible to the process from inflammation to tumorigenesis; Figure S9: Mutations rates of the 20 classes biological processes; Figure S10: Effects of inflammation on population size and DNA damage; Figure S11: Population dynamics with different inflammation conditions; Figure S12: Evolution dynamics from 2 sample runs; Figure S13: Evolution dynamics from under various inflammation conditions; Figure S14: Evolution dynamics from 1 sample runs occurs to a single stem cell; Figure S15: Evolution dynamics from 1 sample runs for a group of stem cells; Figure S16: Summary of the double mutations present at the three time points. Figure S17: Evolution dynamics from 4 sample runs; Figure S18: Evolution dynamics under 5-15 protocols, periodic acute inflammation attacks; and Figure S19: Evolution dynamics under 0-15 protocols, periodic acute inflammation attacks.