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Reconstruction of Transcriptional Regulatory Networks by Stability-Based Network Component Analysis
2013
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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Reliable inference of transcription regulatory networks is still a challenging task in the field of computational biology. ...
Network component analysis (NCA) has become a powerful scheme to uncover the networks behind complex biological processes, especially when gene expression data is integrated with binding motif information ...
Acknowledgments This work was supported by the National Institutes of Health (CA139246, CA149653 CA149147 and NS29525-18A). ...
doi:10.1109/tcbb.2012.146
pmid:24407294
pmcid:PMC3652899
fatcat:tocuoom6m5dtnbmkucjus6kjfy
Enriching for direct regulatory targets in perturbed gene-expression profiles
2004
Genome Biology
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The updated algorithm can process networks containing feedback loops, incorporate positive and negative regulatory relationships during network reconstruction, and utilize data from double mutants to resolve ...
When applied to experimental data the reconstruction procedure preferentially retains direct transcription factor-target relationships. ...
Renaud for hosting S.L.G. in his lab during part of this project. This work was supported by the W. M. Keck Foundation. ...
doi:10.1186/gb-2004-5-4-r29
pmid:15059262
pmcid:PMC395788
fatcat:jj2by66qpjbkbmwfkx55gtp6hu
CRITICAL ANALYSIS OF TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL REGULATORY NETWORKS IN MULTIPLE MYELOMA
[chapter]
2009
Biocomputing 2010
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In this study, critical analysis of network components has been applied to inspect the transcriptional and post-transcriptional regulatory networks reconstructed from mRNA and microRNA expression data ...
The application of critical analysis to transcriptional and post-transcriptional regulatory networks allowed inferring novel regulatory relations potentially functional in multiple myeloma. * These authors ...
Here, the analysis of the network critical components was applied on the nodes of transcriptional and posttranscriptional regulatory networks reconstructed from mRNA and miRNA expression data of multiple ...
doi:10.1142/9789814295291_0042
fatcat:ojvh4ruy5bezpnpyai4u35sfpe
An Evaluation of the Information Technology of Gene Expression Profiles Processing Stability for Different Levels of Noise Components
2018
Data
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The hybrid model of objective clustering based on the SOTA algorithm and the technology of gene regulatory networks reconstruction have been investigated to evaluate the stability to the level of the noise ...
The results of the simulation have shown that the hybrid model of the objective clustering has high level of stability to noise components and vice versa, the technology of gene regulatory networks reconstruction ...
Gene regulatory networks reconstruction and validation of the obtained models The reconstruction of the gene regulatory networks was performed based on the correlation inference algorithm with the use ...
doi:10.3390/data3040048
fatcat:lyo2ezu6hngvbayrjhhdjfsqnu
Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli
2009
BMC Bioinformatics
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We model the integrated regulatory system by a set of biochemical reactions which lead to a log-bilinear problem. ...
In this work, we propose a novel framework to infer the activity of regulators including both TFs and ncRNAs by exploring the expression profiles of target genes and (post)transcriptional regulatory relationships ...
To evaluate the performance of the method, we compared it with those from Network Component Analysis (NCA), Principle Component analysis (PCA), Independent Component Analysis (ICA). ...
doi:10.1186/1471-2105-10-s4-s6
pmid:19426454
pmcid:PMC2681065
fatcat:b5623folo5alhboc63ubqmstq4
Motif-directed network component analysis for regulatory network inference
2008
BMC Bioinformatics
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Network Component Analysis (NCA) has shown its effectiveness in discovering regulators and inferring transcription factor activities (TFAs) when both microarray data and ChIPon-chip data are available. ...
Specifically, motif analysis is used to obtain initial network topology, and stability analysis is developed and applied with mNCA to extract stable TFAs. ...
This article has been published as part of BMC Bioinformatics Volume 9 Supplement 1, 2008: Asia Pacific Bioinformatics Network (APBioNet) Sixth International Conference on Bioinformatics (InCoB2007). ...
doi:10.1186/1471-2105-9-s1-s21
pmid:18315853
pmcid:PMC2259422
fatcat:stxkr4e4uzgslhthrgl3wgbuo4
The Reconstruction of Transcriptional Networks Reveals Critical Genes with Implications for Clinical Outcome of Multiple Myeloma
2011
Clinical Cancer Research
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Critical analysis of network components was applied to identify genes playing an essential role in transcriptional networks, which are conserved between data sets. ...
Experimental Design: Gene regulatory networks were reconstructed by using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) and microarray data from seven MM data sets. ...
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. ...
doi:10.1158/1078-0432.ccr-11-0596
pmid:21890453
fatcat:lna67qkoaveopnlv62fd4whktu
Modelling uncertainty in transcriptome measurements enhances network component analysis of yeast metabolic cycle
2009
2009 IEEE International Conference on Acoustics, Speech and Signal Processing
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the network component analysis (NCA) approach. ...
For several of these we found literature evidence of post-transcriptional regulation. Accounting for probe level uncertainty of microarray measurements leads to improved network component analysis. ...
The technique of Network Component Analysis (NCA) was developed by Liao et al. [2] to achieve the factorization above. ...
doi:10.1109/icassp.2009.4959947
dblp:conf/icassp/ChangHN09
fatcat:5525rmrtbfcevnd6ynsjhdqc34
A differential network analysis approach for lineage specifier prediction in stem cell subpopulations
2015
npj Systems Biology and Applications
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However, the identification of a transcriptional regulatory network (TRN) for each cell subpopulation within a population and genes determining specific cell fates (lineage specifiers) remains a challenge ...
METHODS: The proposed method is based on a model that considers each stem cell subpopulation being in a stable state maintained by its specific TRN stability core, and cell differentiation involves changes ...
analysis (PCA)-based classification of single-cell samples. ...
doi:10.1038/npjsba.2015.12
pmid:28725462
pmcid:PMC5516870
fatcat:n2jvh7el4bbmlnci5i32kgw32a
Reconstruct gene regulatory network using slice pattern model
2009
BMC Genomics
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In order to estimate performances of stability and reliability of our model, an artificial gene network is tested by the traditional linear model and SPM. ...
Under the reliability threshold, θ = 55%, 18 relationships between genes are identified and transcriptional regulatory network is reconstructed. ...
First, the stability of the gene regulatory model reconstructed using SPM is better than those models coming from traditional linear model. ...
doi:10.1186/1471-2164-10-s1-s2
pmid:19594879
pmcid:PMC2709263
fatcat:qribb6z2uzcxvpf2p6r6lgl4gu
Dynamic Regulatory Network Reconstruction for Alzheimer's Disease Based on Matrix Decomposition Techniques
2014
Computational and Mathematical Methods in Medicine
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Based on that, the dynamical gene regulatory networks of the deteriorative courses of AD were reconstructed. ...
In this study, based on DNA microarray gene expression data and a priori information of TFs, network component analysis (NCA) algorithm is applied to determining the TF activities and regulatory influences ...
Acknowledgment This work was supported by the National Natural Science Foundation of China (nos. 61271446 and 61003093). ...
doi:10.1155/2014/891761
pmid:25024739
pmcid:PMC4082865
fatcat:fil45zo64fhlhjt4b3ynnitolm
Integrated Approach in Systems Biology
2014
Computational and Mathematical Methods in Medicine
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understanding of the dynamics of regulatory, signaling, interaction, and metabolic networks through modeling and simulation techniques; (iv) prediction of protein/RNA structure and biological network-based ...
The potential topics include (i) large-scale or cross-species data integration for the reconstruction of networks and pathways; (ii) genomic data analysis using systems biology approaches; (iii) quantitative ...
We would like to acknowledge the organizers and committee members of The Fourth International Workshop on Integrative Data Analysis in Systems Biology (IDASB 2013, in conjunction with IEEE Conference on ...
doi:10.1155/2014/656473
pmid:25628754
pmcid:PMC4297625
fatcat:6w67ie5vhzcajmupvcfkbc5oh4
Analysis of Combinatorial Gene Regulation with Thermodynamic Models
[chapter]
2010
Frontiers in Computational and Systems Biology
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A major challenge in the study of gene regulation is to identify the interaction relationships within a regulatory network and further to reconstruct gene regulatory networks. ...
This network suggests that Oct4, Sox2 and Klf4 indirectly repress lineage specific differentiation genes by activating transcriptional repressors of Ctbp2, Rest and Mtf2. ii ...
Along this line, Network-Identifier is proposed to reconstruct transcription network based on biophysical models of transcription regulation. ...
doi:10.1007/978-1-84996-196-7_1
fatcat:hjpnfhr2svf5him4kkm3mz5trm
Iterative sub-network component analysis enables reconstruction of large scale genetic networks
2015
BMC Bioinformatics
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Network component analysis (NCA) became a popular tool to understand complex regulatory networks. ...
Results: To address this, we developed a novel, Iterative Sub-Network Component Analysis (ISNCA) for reconstructing networks at any size. ...
Similarly, many other pivotal TFs in breast cancer were removed by NCA (Table 2) but retained by ISNCA, which not only reconstructed large gene regulatory networks, but also retained their key components ...
doi:10.1186/s12859-015-0768-9
pmid:26537518
pmcid:PMC4634733
fatcat:2tbkcii6yram3c6dd3z3e4scwa
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states
2005
Proceedings of the National Academy of Sciences of the United States of America
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Here, we use a model of a genome-scale reconstruction of the integrated metabolic and transcriptional regulatory networks for Escherichia coli, composed of 1,010 gene products, to assess the properties ...
The set of all functional states of the integrated network exhibits a discernable structure that can be visualized in 3-dimensional space, showing that the transcriptional regulatory network governing ...
All possible media components (see Data Set 1, which is published as supporting information on the PNAS web site) that can be used by the metabolic and transcriptional regulatory network reconstruction ...
doi:10.1073/pnas.0505231102
pmid:16357206
pmcid:PMC1323155
fatcat:bzbz2y3sjzcohc7nuilrew2zmu
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