Gene regulatory network model

Zixuan Cang; Yangyang Wang; Qixuan Wang; Ken W. Y. Cho; William Holmes; Qing Nie

Improve Research Reproducibility A Bio-protocol resource

Home
Protocols

Concise Method

Gene regulatory network model

ZC Zixuan Cang

YW Yangyang Wang

QW Qixuan Wang

KC Ken W. Y. Cho

WH William Holmes

QN Qing Nie

This method is extracted from research article: PLoS Comput Biol, Mar 2021

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development

DOI: 10.1371/journal.pcbi.1008571

Request a Protocol

Ask a question

Favorite

The gene expression dynamics of Nanog/Gata6/Fgf are represented by the following non-dimensional stochastic ODE system:

where [Nan]_i, [Gat]_i, [Fr]_i, [Fs]_i, and [Erk]_i represent secreted Nanog, Gata6, Fgfr2, Fgf4, and Erk in cell i. The perceived Fgf4 from neighboring cells for cell i is described by

where r_contact is a cutoff determining if cells located at r_i and r_j are neighboring cells, N_j is the number of neighbors of cell j, and γ_j is a Gaussian noise.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

Post a Question

0 Q&A

Share your protocol with your peers.

Submit a Preprint Protocol