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Reconstruction of Transcriptional Regulatory Networks by Stability-Based Network Component Analysis

Xi Chen, Jianhua Xuan, Chen Wang, Ayesha N. Shajahan, Rebecca B. Riggins, Robert Clarke
2013 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

Susannah G Tringe, Andreas Wagner, Stephanie W Ruby
2004 Genome Biology  
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]

MARTA BIASIOLO, MATTIA FORCATO, LINO POSSAMAI, FRANCESCO FERRARI, LUCA AGNELLI, MARTA LIONETTI, KATIA TODOERTI, ANTONINO NERI, MASSIMO MARCHIORI, STEFANIA BORTOLUZZI, SILVIO BICCIATO
2009 Biocomputing 2010  
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

Sergii Babichev
2018 Data  
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

Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen
2009 BMC Bioinformatics  
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

Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke, Eric Hoffman
2008 BMC Bioinformatics  
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

L. Agnelli, M. Forcato, F. Ferrari, G. Tuana, K. Todoerti, B. A. Walker, G. J. Morgan, L. Lombardi, S. Bicciato, A. Neri
2011 Clinical Cancer Research  
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

C.Q. Chang, Y.S. Hung, M. Niranjan
2009 2009 IEEE International Conference on Acoustics, Speech and Signal Processing  
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

Satoshi Okawa, Vladimir Espinosa Angarica, Ihor Lemischka, Kateri Moore, Antonio del Sol
2015 npj Systems Biology and Applications  
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

Yadong Wang, Guohua Wang, Bo Yang, Haijun Tao, Jack Y Yang, Youping Deng, Yunlong Liu
2009 BMC Genomics  
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

Wei Kong, Xiaoyang Mou, Xing Zhi, Xin Zhang, Yang Yang
2014 Computational and Mathematical Methods in Medicine  
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

Huiru Zheng, Rui Jiang, Zhongming Zhao
2014 Computational and Mathematical Methods in Medicine  
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]

Chieh-Chun Chen, Sheng Zhong
2010 Frontiers in Computational and Systems Biology  
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

Naresh Doni Jayavelu, Lasse S. Aasgaard, Nadav Bar
2015 BMC Bioinformatics  
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

C. L. Barrett, C. D. Herring, J. L. Reed, B. O. Palsson
2005 Proceedings of the National Academy of Sciences of the United States of America  
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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