A non-linear reverse-engineering method for inferring genetic regulatory networks
Hematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made...
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PeerJ Inc.
2020-04-01
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| Online Access: | https://peerj.com/articles/9065.pdf |
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| author | Siyuan Wu Tiangang Cui Xinan Zhang Tianhai Tian |
| author_facet | Siyuan Wu Tiangang Cui Xinan Zhang Tianhai Tian |
| author_sort | Siyuan Wu |
| collection | DOAJ |
| description | Hematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made for understanding hematopoiesis, the detailed regulatory mechanisms for the fate determination of HSCs are still unraveled. In this study, we propose a novel approach to infer the detailed regulatory mechanisms. This work is designed to develop a mathematical framework that is able to realize nonlinear gene expression dynamics accurately. In particular, we intended to investigate the effect of possible protein heterodimers and/or synergistic effect in genetic regulation. This approach includes the Extended Forward Search Algorithm to infer network structure (top-down approach) and a non-linear mathematical model to infer dynamical property (bottom-up approach). Based on the published experimental data, we study two regulatory networks of 11 genes for regulating the erythrocyte differentiation pathway and the neutrophil differentiation pathway. The proposed algorithm is first applied to predict the network topologies among 11 genes and 55 non-linear terms which may be for heterodimers and/or synergistic effect. Then, the unknown model parameters are estimated by fitting simulations to the expression data of two different differentiation pathways. In addition, the edge deletion test is conducted to remove possible insignificant regulations from the inferred networks. Furthermore, the robustness property of the mathematical model is employed as an additional criterion to choose better network reconstruction results. Our simulation results successfully realized experimental data for two different differentiation pathways, which suggests that the proposed approach is an effective method to infer the topological structure and dynamic property of genetic regulations. |
| first_indexed | 2024-03-09T07:03:20Z |
| format | Article |
| id | doaj.art-84efc6090fcc4ddb8c57dde700156940 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:03:20Z |
| publishDate | 2020-04-01 |
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| spelling | doaj.art-84efc6090fcc4ddb8c57dde7001569402023-12-03T09:48:12ZengPeerJ Inc.PeerJ2167-83592020-04-018e906510.7717/peerj.9065A non-linear reverse-engineering method for inferring genetic regulatory networksSiyuan Wu0Tiangang Cui1Xinan Zhang2Tianhai Tian3School of Mathematics, Monash University, Clayton, VIC, AustraliaSchool of Mathematics, Monash University, Clayton, VIC, AustraliaSchool of Mathematics and Statistics, Central China Normal University, Wuhan, PR ChinaSchool of Mathematics, Monash University, Clayton, VIC, AustraliaHematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made for understanding hematopoiesis, the detailed regulatory mechanisms for the fate determination of HSCs are still unraveled. In this study, we propose a novel approach to infer the detailed regulatory mechanisms. This work is designed to develop a mathematical framework that is able to realize nonlinear gene expression dynamics accurately. In particular, we intended to investigate the effect of possible protein heterodimers and/or synergistic effect in genetic regulation. This approach includes the Extended Forward Search Algorithm to infer network structure (top-down approach) and a non-linear mathematical model to infer dynamical property (bottom-up approach). Based on the published experimental data, we study two regulatory networks of 11 genes for regulating the erythrocyte differentiation pathway and the neutrophil differentiation pathway. The proposed algorithm is first applied to predict the network topologies among 11 genes and 55 non-linear terms which may be for heterodimers and/or synergistic effect. Then, the unknown model parameters are estimated by fitting simulations to the expression data of two different differentiation pathways. In addition, the edge deletion test is conducted to remove possible insignificant regulations from the inferred networks. Furthermore, the robustness property of the mathematical model is employed as an additional criterion to choose better network reconstruction results. Our simulation results successfully realized experimental data for two different differentiation pathways, which suggests that the proposed approach is an effective method to infer the topological structure and dynamic property of genetic regulations.https://peerj.com/articles/9065.pdfGenetic regulatory networkNetwork inferenceHematopoiesisProbabilistic graphic modelDifferential equation |
| spellingShingle | Siyuan Wu Tiangang Cui Xinan Zhang Tianhai Tian A non-linear reverse-engineering method for inferring genetic regulatory networks PeerJ Genetic regulatory network Network inference Hematopoiesis Probabilistic graphic model Differential equation |
| title | A non-linear reverse-engineering method for inferring genetic regulatory networks |
| title_full | A non-linear reverse-engineering method for inferring genetic regulatory networks |
| title_fullStr | A non-linear reverse-engineering method for inferring genetic regulatory networks |
| title_full_unstemmed | A non-linear reverse-engineering method for inferring genetic regulatory networks |
| title_short | A non-linear reverse-engineering method for inferring genetic regulatory networks |
| title_sort | non linear reverse engineering method for inferring genetic regulatory networks |
| topic | Genetic regulatory network Network inference Hematopoiesis Probabilistic graphic model Differential equation |
| url | https://peerj.com/articles/9065.pdf |
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