scholarly journals A novel method of gene regulatory network structure inference from gene knock-out expression data

2019 ◽  
Vol 24 (4) ◽  
pp. 446-455 ◽  
Author(s):  
Xiang Chen ◽  
Min Li ◽  
Ruiqing Zheng ◽  
Siyu Zhao ◽  
Fang-Xiang Wu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Network Structure ◽  
Regulatory Network ◽  
Expression Data ◽  
Knock Out ◽  
Novel Method ◽  
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 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.

PAGeneRN

2020 ◽  
pp. 1052-1075 ◽  
Author(s):  
Dina Elsayad ◽  
A. Ali ◽  
Howida A. Shedeed ◽  
Mohamed F. Tolba
Keyword(s):  
Gene Expression ◽  
Data Analysis ◽  
Network Analysis ◽  
Gene Regulatory Network ◽  
Gene Expression Data ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Expression Data ◽  
Gene Expression Data Analysis ◽  
Gene Regulatory

The gene expression analysis is an important research area of Bioinformatics. The gene expression data analysis aims to understand the genes interacting phenomena, gene functionality and the genes mutations effect. The Gene regulatory network analysis is one of the gene expression data analysis tasks. Gene regulatory network aims to study the genes interactions topological organization. The regulatory network is critical for understanding the pathological phenotypes and the normal cell physiology. There are many researches that focus on gene regulatory network analysis but unfortunately some algorithms are affected by data size. Where, the algorithm runtime is proportional to the data size, therefore, some parallel algorithms are presented to enhance the algorithms runtime and efficiency. This work presents a background, mathematical models and comparisons about gene regulatory networks analysis different techniques. In addition, this work proposes Parallel Architecture for Gene Regulatory Network (PAGeneRN).

scholarly journals Approximated Gene Expression Trajectories (AGETs) for Gene Regulatory Network Inference on Cell Tracks

2022 ◽  
Author(s):  
Kay Spiess ◽  
Timothy Fulton ◽  
Seogwon Hwang ◽  
Kane Toh ◽  
Dillan Saunders ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pattern Formation ◽  
Gene Regulatory Network ◽  
Gene Expression Data ◽  
Regulatory Network ◽  
Quantitative Data ◽  
Expression Data ◽  
Cell Movements ◽  
Reverse Engineer ◽  
Gene Regulatory

The study of pattern formation has benefited from reverse-engineering gene regulatory network (GRN) structure from spatio-temporal quantitative gene expression data. Traditional approaches omit tissue morphogenesis, hence focusing on systems where the timescales of pattern formation and morphogenesis can be separated. In such systems, pattern forms as an emergent property of the underlying GRN. This is not the case in many animal patterning systems, where patterning and morphogenesis are simultaneous. To address pattern formation in these systems we need to adapt our methodologies to explicitly accommodate cell movements and tissue shape changes. In this work we present a novel framework to reverse-engineer GRNs underlying pattern formation in tissues experiencing morphogenetic changes and cell rearrangements. By combination of quantitative data from live and fixed embryos we approximate gene expression trajectories (AGETs) in single cells and use a subset to reverse-engineer candidate GRNs using a Markov Chain Monte Carlo approach. GRN fit is assessed by simulating on cell tracks (live-modelling) and comparing the output to quantitative data-sets. This framework outputs candidate GRNs that recapitulate pattern formation at the level of the tissue and the single cell. To our knowledge, this inference methodology is the first to integrate cell movements and gene expression data, making it possible to reverse-engineer GRNs patterning tissues undergoing morphogenetic changes.

scholarly journals Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

2020 ◽  
Author(s):  
Xizhi Li ◽  
Min Li ◽  
Beibei Zhou ◽  
Jinlin Bao ◽  
Liang Zhu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Leaf Development ◽  
Regulatory Network ◽  
Leaf Rolling ◽  
Knock Out ◽  
Genome Wide ◽  
Leaf Transcriptome ◽  
Dna Insertion ◽  
Gene Regulatory ◽  
Cuticle Development

Abstract Background SRL1 (SEMI-ROLLED LEAF 1) also named as CLD1 (CURLED LEAF AND DWARF 1), encoding a putative glyphopholipidininol-anchored membrane protein, has been characterized as a gene involved in the regulation of leaf morphology in rice. Mutants of srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit defects in leaf development resulting in a phenotype with adaxially rolled leaves. Results To explore the gene regulatory network of leaf development that controlled by SRL1 in rice, we created a homozygous SRL1 knock out (KO) line by CRISPR/Cas9, which showed defects in leaf development with adaxially rolling. By comparing the leaf transcriptome of a homozygous SRL1 KO line (srl1-KO) with the control, a total number of 3,178 genes were identified as differentially expressed genes, of which 1,216 genes were significantly up regulated, while 1,962 genes were down regulated. Further analyses indicated that, a group of known leaf rolling related genes, which involved in bulliform cells and cuticle development such as OsZHD1, OsLBD3-7, RFS, ACL1, CFL1, SND1, OsCESA5 and OsCESA6 were up or down regulated in the srl1-KO. Conclusions SRL1 might control leaf rolling by regulating a couple of genes that affecting cytological architecture of leaf cells such as bulliforms and cuticle of leaves.

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