Background: One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental data and/or educated guesses, which can be time-consuming and error-prone, especially for large networks.
Results: We present a user-friendly computational tool for the community to use our newly developed method named random circuit perturbation (RACIPE), to explore the robust dynamical features of gene regulatory circuits without the requirement of detailed kinetic parameters. Taking the network topology as the only input, RACIPE generates an ensemble of circuit models with distinct randomized parameters and uniquely identifies robust dynamical properties by statistical analysis. Here, we discuss the implementation of the software and the statistical analysis methods of RACIPE-generated data to identify robust gene expression patterns and the functions of genes and regulatory links. Finally, we apply the tool on coupled toggle-switch circuits and a published circuit of B-lymphopoiesis.
Conclusions: We expect our new computational tool to contribute to a more comprehensive and unbiased understanding of mechanisms underlying gene regulatory networks. RACIPE is a free open source software distributed under (Apache 2.0) license and can be downloaded from GitHub ( https://github.com/simonhb1990/RACIPE-1.0 ).
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http://dx.doi.org/10.1186/s12918-018-0594-6 | DOI Listing |
Crohn's disease (CD) is a complex inflammatory bowel disease resulting from an interplay of genetic, microbial, and environmental factors. Cell-type-specific contributions to CD etiology and genetic risk are incompletely understood. Here we built a comprehensive atlas of cell-type- resolved chromatin accessibility comprising 557,310 candidate cis-regulatory elements (cCREs) in terminal ileum and ascending colon from patients with active and inactive CD and healthy controls.
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View Article and Find Full Text PDFFront Plant Sci
December 2024
Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, Guangdong, China.
In tea (), anthocyanins are important secondary metabolites that are linked to leaf color. Anthocyanin biosynthesis is a complex biological process, in which multiple genes including structural and regulatory genes are involved. Here, we describe the cloning and characterizing of a new R2R3-MYB transcription factor gene, , isolated from purple tea variety ''.
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View Article and Find Full Text PDFAnn Med
December 2025
Department of Breast Surgery, Second Affiliated Hospital and Cancer Institute (Provincial Key Laboratory of Tumor Microenvironment and Immunotherapy, Key Laboratory of Cancer Prevention & Intervention, National Ministry of Education), Zhejiang University School of Medicine, Hangzhou, China.
Background: Quaking (QKI) is a member of the signal transduction and activators of RNA (STAR) family, performing a crucial multifunctional regulatory role in alternative splicing, mRNA precursor processing, mRNA transport and localization, mRNA stabilization, and translation during tumour progression. Abnormal QKI expression or fusion mutations lead to aberrant RNA and protein expression, thereby promoting tumour progression. However, in many types of tumour, QKI played a role as tumour suppressor, the regulatory role of QKI in tumour progression remains ambiguous.
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