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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  
We incorporated probe level uncertainties in gene expression measurements into the NCA analysis by the application of probabilistic principal component analysis (PPCA), and applied the method to data from  ...  the network component analysis (NCA) approach.  ...  We have used probabilistic principal component analysis to propagate probe level uncertainty in microarray measurements through such network analysis.  ... 
doi:10.1109/icassp.2009.4959947 dblp:conf/icassp/ChangHN09 fatcat:5525rmrtbfcevnd6ynsjhdqc34

A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism) [chapter]

Evangelos Simeonidis, Sriram Chandrasekaran, Nathan D. Price
2013 Msphere  
Here, we present a guide to PROM (probabilistic regulation of metabolism), an automated method for the construction and simulation of integrated metabolic and transcriptional regulatory networks that enables  ...  The integration of transcriptional regulatory and metabolic networks is a crucial step in the process of predicting metabolic behaviors that emerge from either genetic or environmental changes.  ...  From these data, the transcriptional regulatory network of the organism can be quantified statistically, similar to the probabilistic Boolean networks of Shmulevich et al. (20) .  ... 
doi:10.1007/978-1-62703-299-5_6 pmid:23417801 fatcat:dajvwggo2ng5xpjgmenkh5filu

Network-based approaches for analysis of complex biological systems

Deborah Chasman, Alireza Fotuhi Siahpirani, Sushmita Roy
2016 Current Opinion in Biotechnology  
functions (reviewed by Kim et al. [11]). 30 Expression-based network inference has been approached in two ways: by reconstructing regulatory programs for (i) individual genes at a time ("per-gene" methods  ...  Towards this end, Arrieta-Ortiz and Hafemeister et. al. [23] first use network component analysis [24] to predict the activity of TFs given a prior network, and then use these TF activities to predict  ...  Network component analysis: reconstruction of regulatory signals in biological systems. Proceedings of the National Academy of Sciences 2003;100(26):15522-15527. doi:10.1073/pnas.2136632100. 25.  ... 
doi:10.1016/j.copbio.2016.04.007 pmid:27115495 fatcat:3ppskhtoifbobayer5bzpqz6qq

Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks

Hanen Mhamdi, Jérémie Bourdon, Abdelhalim Larhlimi, Mourad Elloumi
2020 Informatics  
Thus, the integration of the transcriptional regulatory information is required to improve the accuracy and predictive ability of metabolic models.  ...  In this paper, we propose an integrative predictive model based on techniques combining semantic web, probabilistic modeling, and constraint-based modeling methods.  ...  Reconstruction of Regulatory Networks A crucial step in our integrated model is the reconstruction of the transcriptional regulatory network.  ... 
doi:10.3390/informatics7010001 fatcat:plvr2d64qzdxnp77wbsdia5qtm

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

Dawn Thompson, Aviv Regev, Sushmita Roy
2015 Annual Review of Cell and Developmental Biology  
Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequences to functional data.  ...  In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level.  ...  D.T. is supported by the NIH (R01CA119176-01). A.R. is supported by HHMI, the NIH (R01CA119176-01, P50HG006193), and the Sloan Foundation.  ... 
doi:10.1146/annurev-cellbio-100913-012908 pmid:26355593 fatcat:sryxj3e2gvapnnnkmnzdhnyzr4

Data-driven integration of genome-scale regulatory and metabolic network models

Saheed Imam, Sascha Schäuble, Aaron N. Brooks, Nitin S. Baliga, Nathan D. Price
2015 Frontiers in Microbiology  
Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years.  ...  Citation: Imam S, Schäuble S, Brooks AN, Baliga NS and Price ND (2015) Data-driven integration of genome-scale regulatory and metabolic network models. Front. Microbiol. 6:409.  ...  Acknowledgments This work was funded in part by DOE-ABY (DEEE0006315) (NSB, NDP), DOE ARPA-E program (DE-AR0000426) (NDP),  ... 
doi:10.3389/fmicb.2015.00409 pmid:25999934 pmcid:PMC4419725 fatcat:vp3skde33rgs3asbda7vhgrqly

Reconstruction of microbial transcriptional regulatory networks

Markus J Herrgård, Markus W Covert, Bernhard Ø Palsson
2004 Current Opinion in Biotechnology  
Although metabolic networks can be readily reconstructed through comparative genomics, the reconstruction of regulatory networks has been hindered by the relatively low level of evolutionary conservation  ...  This data together with literature-derived knowledge has opened the way for genome-scale reconstruction of transcriptional regulatory networks.  ...  By contrast, the two primary data types useful for the regulatory network reconstruction taskgenome-wide mRNA expression and location analysis data -are widely available.  ... 
doi:10.1016/j.copbio.2003.11.002 pmid:15102470 fatcat:zzadypbtcbchzdtwz7xyzbgaq4

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

Sriram Chandrasekaran, Nathan D. Price
2010 Proceedings of the National Academy of Sciences of the United States of America  
Metabolic networks are typically reconstructed and analyzed by using detailed chemistry-based methods (1, 2), whereas transcriptional regulatory networks have typically been reconstructed based on high-throughput  ...  bridging two important classes of systems biology models that are rarely combined quantitatively. constraint-based modeling | flux balance analysis | metabolic networks | transcriptional regulation | probabilistic  ...  This work was supported by a National Institutes of Health/National Cancer Institute Howard Temin Pathway to Independence Award in Cancer Research, a Young Investigator Grant from the Roy J.  ... 
doi:10.1073/pnas.1005139107 pmid:20876091 pmcid:PMC2955152 fatcat:zh7slr2mgvd4hle2k3vtbk5bwq

Reconstruction of biochemical networks in microorganisms

Adam M. Feist, Markus J. Herrgård, Ines Thiele, Jennie L. Reed, Bernhard Ø. Palsson
2008 Nature Reviews Microbiology  
network components.  ...  Such studies are enabled by reconstruction, at the genomic scale, of the biochemical reaction networks that underlie cellular processes.  ...  A.M.F. and I.T. were supported by National Institutes of Health (NIH) grant R01 GM057089 and M.J.H. was supported by NIH grant R01 GM071808.  ... 
doi:10.1038/nrmicro1949 pmid:19116616 pmcid:PMC3119670 fatcat:rzxjs54qizdl7gnzjeuisc6lw4


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

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.  ...  This work was supported by the W. M. Keck Foundation.  ... 
doi:10.1186/gb-2004-5-4-r29 pmid:15059262 pmcid:PMC395788 fatcat:jj2by66qpjbkbmwfkx55gtp6hu

A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks

Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva, Riccardo Bellazzi
2020 BMC Bioinformatics  
network reconstruction algorithms.  ...  Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology.  ...  Decomposition of a genome-wide Transcriptional Regulatory Network (TRN) allows to operate on the TF-TF Component, characterized by many regulatory loops, e.g. feedback loop (as shown in the magnifying  ... 
doi:10.1186/s12859-020-3510-1 pmid:32471360 fatcat:3v6orxxiyjaktmui6opbjebrxm

Iterative Reconstruction of Transcriptional Regulatory Networks: an Algorithmic Approach

Christian Barrett, Bernhard O. Palsson
2005 PLoS Computational Biology  
Principal among these will be transcriptional regulatory networks.  ...  This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks.  ...  CLB conceived and designed the experiments, performed the experiments, analyzed the data, and contributed reagents/materials/analysis tools. BOP made the work possible by having a lab.  ... 
doi:10.1371/journal.pcbi.0020052.eor fatcat:7iromi42jbbh5kbh5bidixkyea

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach

Christian L. Barrett, Bernhard O. Palsson
2006 PLoS Computational Biology  
Principal among these will be transcriptional regulatory networks.  ...  This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks.  ...  CLB conceived and designed the experiments, performed the experiments, analyzed the data, and contributed reagents/materials/analysis tools. BOP made the work possible by having a lab.  ... 
doi:10.1371/journal.pcbi.0020052 pmid:16710450 pmcid:PMC1463018 fatcat:bbxcn27ibngqlgawcffnjkp2oq

Inferring gene regulatory networks by thermodynamic modeling

Chieh-Chun Chen, Sheng Zhong
2008 BMC Genomics  
To date, the reconstruction of gene regulatory networks from gene expression data has primarily relied on the correlation between the expression of transcription regulators and that of target genes.  ...  This network suggests that Oct4, Sox2 and Klf4 indirectly repress lineage specific differentiation genes by activating transcriptional repressors of Ctbp2, Rest and Mtf2.  ...  Acknowledgements This work is supported by National Center for Supercomputing Applications (SZ).  ... 
doi:10.1186/1471-2164-9-s2-s19 pmid:18831784 pmcid:PMC2559883 fatcat:gg7cpggfofbrzmlbnmm3eoor4u
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