scholarly journals Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network

Development ◽  
2007 ◽  
Vol 134 (17) ◽  
pp. 3077-3087 ◽  
Author(s):  
C. A. Ettensohn ◽  
C. Kitazawa ◽  
M. S. Cheers ◽  
J. D. Leonard ◽  
T. Sharma
Keyword(s):  
Gene Regulatory Network ◽  
Sea Urchin ◽  
Gene Regulatory Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Developmental Plasticity ◽  
Sea Urchin Embryo ◽  
Gene Regulatory

scholarly journals Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm

RSC Advances ◽  
2017 ◽  
Vol 7 (37) ◽  
pp. 23222-23233 ◽  
Author(s):  
Wei Liu ◽  
Wen Zhu ◽  
Bo Liao ◽  
Haowen Chen ◽  
Siqi Ren ◽  
...  
Keyword(s):  
Systems Biology ◽  
Gene Regulatory Network ◽  
Gene Regulatory Networks ◽  
Network Structure ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Central Problem ◽  
Expression Data ◽  
Redundancy Reduction ◽  
Gene Regulatory

Inferring gene regulatory networks from expression data is a central problem in systems biology.

scholarly journals Activation of the skeletogenic gene regulatory network in the early sea urchin embryo

Development ◽  
2010 ◽  
Vol 137 (7) ◽  
pp. 1149-1157 ◽  
Author(s):  
T. Sharma ◽  
C. A. Ettensohn
Keyword(s):  
Gene Regulatory Network ◽  
Sea Urchin ◽  
Regulatory Network ◽  
Sea Urchin Embryo ◽  
Gene Regulatory

scholarly journals Specific functions of the Wnt signaling system in gene regulatory networks throughout the early sea urchin embryo

2014 ◽  
Vol 111 (47) ◽  
pp. E5029-E5038 ◽  
Author(s):  
Miao Cui ◽  
Natnaree Siriwon ◽  
Enhu Li ◽  
Eric H. Davidson ◽  
Isabelle S. Peter
Keyword(s):  
Wnt Signaling ◽  
Sea Urchin ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Signaling System ◽  
Sea Urchin Embryo ◽  
Gene Regulatory

scholarly journals Predicting genotype-specific gene regulatory networks

2021 ◽  
Author(s):  
Deborah Weighill ◽  
Marouen Ben Guebila ◽  
Kimberly Glass ◽  
John Quackenbush ◽  
John Platig
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Gene Regulatory Networks ◽  
Genetic Variants ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Specific Gene ◽  
Disease Etiology ◽  
Gene Regulatory ◽  
The Impact

AbstractThe majority of disease-associated genetic variants are thought to have regulatory effects, including the disruption of transcription factor (TF) binding and the alteration of downstream gene expression. Identifying how a person’s genotype affects their individual gene regulatory network has the potential to provide important insights into disease etiology and to enable improved genotype-specific disease risk assessments and treatments. However, the impact of genetic variants is generally not considered when constructing gene regulatory networks. To address this unmet need, we developed EGRET (Estimating the Genetic Regulatory Effect on TFs), which infers a genotype-specific gene regulatory network (GRN) for each individual in a study population by using message passing to integrate genotype-informed TF motif predictions - derived from individual genotype data, the predicted effects of variants on TF binding and gene expression, and TF motif predictions - with TF protein-protein interactions and gene expression. Comparing EGRET networks for two blood-derived cell lines identified genotype-associated cell-line specific regulatory differences which were subsequently validated using allele-specific expression, chromatin accessibility QTLs, and differential TF binding from ChIP-seq. In addition, EGRET GRNs for three cell types across 119 individuals captured regulatory differences associated with disease in a cell-type-specific manner. Our analyses demonstrate that EGRET networks can capture the impact of genetic variants on complex phenotypes, supporting a novel fine-scale stratification of individuals based on their genetic background. EGRET is available through the Network Zoo R package (netZooR v0.9; netzoo.github.io).

scholarly journals Neural Gene Network Constructor: A Neural Based Model for Reconstructing Gene Regulatory Network

2019 ◽  
Author(s):  
Zhang Zhang ◽  
Lifei Wang ◽  
Shuo Wang ◽  
Ruyi Tao ◽  
Jingshu Xiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Network Structure ◽  
Regulatory Network ◽  
Gene Network ◽  
Regulatory Networks ◽  
Expression Data ◽  
Gene Regulatory

SummaryReconstructing gene regulatory networks (GRNs) and inferring the gene dynamics are important to understand the behavior and the fate of the normal and abnormal cells. Gene regulatory networks could be reconstructed by experimental methods or from gene expression data. Recent advances in Single Cell RNA sequencing technology and the computational method to reconstruct trajectory have generated huge scRNA-seq data tagged with additional time labels. Here, we present a deep learning model “Neural Gene Network Constructor” (NGNC), for inferring gene regulatory network and reconstructing the gene dynamics simultaneously from time series gene expression data. NGNC is a model-free heterogenous model, which can reconstruct any network structure and non-linear dynamics. It consists of two parts: a network generator which incorporating gumbel softmax technique to generate candidate network structure, and a dynamics learner which adopting multiple feedforward neural networks to predict the dynamics. We compare our model with other well-known frameworks on the data set generated by GeneNetWeaver, and achieve the state of the arts results both on network reconstruction and dynamics learning.

scholarly journals Early asymmetric cues triggering the dorsal/ventral gene regulatory network of the sea urchin embryo

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Vincenzo Cavalieri ◽  
Giovanni Spinelli
Keyword(s):  
Gene Regulatory Network ◽  
Sea Urchin ◽  
Regulatory Network ◽  
Ectopic Expression ◽  
Paracentrotus Lividus ◽  
Loss Of Function ◽  
Mapk Activity ◽  
Sea Urchin Embryo ◽  
Gene Regulatory ◽  
Dorsal Cells

Dorsal/ventral (DV) patterning of the sea urchin embryo relies on a ventrally-localized organizer expressing Nodal, a pivotal regulator of the DV gene regulatory network. However, the inceptive mechanisms imposing the symmetry-breaking are incompletely understood. In Paracentrotus lividus, the Hbox12 homeodomain-containing repressor is expressed by prospective dorsal cells, spatially facing and preceding the onset of nodal transcription. We report that Hbox12 misexpression provokes DV abnormalities, attenuating nodal and nodal-dependent transcription. Reciprocally, impairing hbox12 function disrupts DV polarity by allowing ectopic expression of nodal. Clonal loss-of-function, inflicted by blastomere transplantation or gene-transfer assays, highlights that DV polarization requires Hbox12 action in dorsal cells. Remarkably, the localized knock-down of nodal restores DV polarity of embryos lacking hbox12 function. Finally, we show that hbox12 is a dorsal-specific negative modulator of the p38-MAPK activity, which is required for nodal expression. Altogether, our results suggest that Hbox12 function is essential for proper positioning of the DV organizer.

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