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Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

Feng Gao, Barrett C Foat, Harmen J Bussemaker
2004 BMC Bioinformatics  
We present MA-Networker, an algorithm that combines microarray data for mRNA expression and transcription factor occupancy to define the regulatory network of the cell.  ...  Multivariate regression analysis is used to infer the activity of each transcription factor, and the correlation across different conditions between this activity and the mRNA expression of a gene is interpreted  ...  B.C.F. and H.J.B. were partially funded by the National Institutes of Health.  ... 
doi:10.1186/1471-2105-5-31 pmid:15113405 pmcid:PMC407845 fatcat:zfnndr5h6rejfa3ju2blencqui

A systems view of mRNP biology

H. Hieronymus
2004 Genes & Development  
Gene expression occurs through a complex mRNA-protein (mRNP) system that stretches from transcription to translation.  ...  Such work has begun to lay the foundation for a broader, integrated view of mRNP organization in gene expression.  ...  Auld, and A. McKee for comments on the manuscript. H. Hieronymus is supported by a Howard Hughes Medical Institute fellowship, and P.A. Silver is supported by NIH grants.  ... 
doi:10.1101/gad.1256904 pmid:15574591 fatcat:o3oqruylrnfsfaka24fcultxha

How to interpret and integrate multi-omics data at systems level

Gun Tae Jung, Kwang-Pyo Kim, Kwoneel Kim
2020 Animal Cells and Systems  
In this review, we discuss how to interpret and integrate multi-omics data systematically using recent studies.  ...  We, therefore, have to not only interpret each single omics layer but also to integrate multi-omics layers systematically to get a full picture of the regulatory landscape of the biological phenotype.  ...  Diagram for integrative network modeling for multi-omics data according to the gene expression process.  ... 
doi:10.1080/19768354.2020.1721321 pmid:32158610 pmcid:PMC7048189 fatcat:txm7cokg3zfzroyo4m2jfyvl7u

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

Sara J.C. Gosline, Allan M. Gurtan, Courtney K. JnBaptiste, Andrew Bosson, Pamela Milani, Simona Dalin, Bryan J. Matthews, Yoon S. Yap, Phillip A. Sharp, Ernest Fraenkel
2016 Cell Reports  
ACKNOWLEDGMENTS The authors thank members of the E.F. and P.A.S. labs for useful discussions about this work.  ...  DB1-0821391, and A.M.G. was supported by the Leukemia and Lymphoma Society grant 5198-09.  ...  Network Integration Small RNA expression levels, iCLIP binding levels, mature mRNA expression levels, ChIP-seq binding data, and intronic RNA expression changes were encoded in a graphical model depicted  ... 
doi:10.1016/j.celrep.2015.12.031 pmid:26748710 pmcid:PMC4831719 fatcat:rhtuz7nemjbljpypqjcsjp2g6y

A framework for integrative analysis of transcriptional and post-transcriptional gene regulation

Hasan Ogul, Giray S. Ozcan
2013 2013 7th International Conference on Application of Information and Communication Technologies  
The framework uses paired samples of mRNA and microRNA expressions and their sequence data to produce low-level regulatory circuits in addition to the coregulated entities of mRNAs, microRNAs and transcription  ...  Here, we propose an approach for simultaneous modeling of transcriptional and post-transcriptional gene regulation over a Bayesian module network.  ...  First, it can model transcriptional and post-transcriptional regulation in a single view by integrating the data of mRNA expressions and mRNA expression if their paired samples are available.  ... 
doi:10.1109/icaict.2013.6722723 fatcat:xpxv7ls7tfgmtoaajeqm66bskq

Network-based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Amanda J. Kedaigle
2017 Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17  
There are also methods that map mRNA expression datasets to protein interaction networks ( MATISSE [30]), methods that identify transcription factor binding sites from epigenetic data (Centipede [22] and  ...  Instead, Omics Integrator combines such transcriptional data with epigenetic data to identify putative changes in the activity of DNA binding proteins that influence transcriptional changes [16] .  ...  Acknowledgments We thank all the beta testers for running the software, in particular Jonathon Gulliver for his evaluation of the test procedures. Author Contributions  ... 
doi:10.1145/3107411.3107461 dblp:conf/bcb/Kedaigle17 fatcat:vur2d3x6sna33g7ikxe5tutj4e

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Nurcan Tuncbag, Sara J. C. Gosline, Amanda Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel, Andreas Prlic
2016 PLoS Computational Biology  
There are also methods that map mRNA expression datasets to protein interaction networks ( MATISSE [30]), methods that identify transcription factor binding sites from epigenetic data (Centipede [22] and  ...  Instead, Omics Integrator combines such transcriptional data with epigenetic data to identify putative changes in the activity of DNA binding proteins that influence transcriptional changes [16] .  ...  Acknowledgments We thank all the beta testers for running the software, in particular Jonathon Gulliver for his evaluation of the test procedures. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004879 pmid:27096930 pmcid:PMC4838263 fatcat:sq7dszd5ifffhckzecrayihcdu

Predicting Phenotype from Genotype Through Automatically Composed Petri Nets [article]

Mary Ann Blätke, Monika Heiner, Wolfgang Marwan
2012 arXiv   pre-print
We describe a modular modelling approach permitting curation, updating, and distributed development of modules through joined community effort overcoming the problem of keeping a combinatorially exploding  ...  Automatically assembled executable models may then consider cell type-specific gene expression patterns and the resulting protein concentrations.  ...  By binding to the promotor region of the gene, these factors form a multimeric protein complex, as shown for transcription factors TF1 and TF2, both of which directly bind to the promotor (b).  ... 
arXiv:1205.4632v1 fatcat:zbv2mnwlf5byrc5dwng7fhghii

Strategies to discover regulatory circuits of the mammalian immune system

Ido Amit, Aviv Regev, Nir Hacohen
2011 Nature reviews. Immunology  
Here, we review approaches for the reconstruction of signalling and transcriptional networks, with a focus on applications in the mammalian innate immune system.  ...  Cells of the immune system provide a particularly useful model for developing and applying such approaches.  ...  Acknowledgments The authors would like to thank the NIH, HHMI, HFSP and the Broad Institute for funding the work presented here.  ... 
doi:10.1038/nri3109 pmid:22094988 pmcid:PMC3747038 fatcat:ye7fokg7l5bo3e4xyxdlqdgazq

Systems perspectives on mRNA processing

Adrienne E McKee, Pamela A Silver
2007 Cell Research  
In parallel, we examine genome-scale investigations that have expanded our knowledge of RNA-binding proteins and the networks of mRNAs that they regulate.  ...  Large-scale systems analyses of mRNA-protein interactions and mRNA dynamics have revealed specificity in mRNA transcription, splicing, transport, translation, and turnover, and have begun to make connections  ...  Acknowledgments We thank members of the Silver lab for their comments and input in writing this manuscript. We also apologize to our colleagues whose work we were unable to highlight.  ... 
doi:10.1038/cr.2007.54 pmid:17621309 fatcat:cgj4oyd65jcthd32s3sgwbxsvq

Toward a complete in silico , multi-layered embryonic stem cell regulatory network

Huilei Xu, Christoph Schaniel, Ihor R. Lemischka, Avi Ma'ayan
2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Recent studies have shown that adult mouse and human cells can be 'reprogrammed' into an induced pluripotent stem (iPS) cell state using simple combinations of transcription factors.  ...  First, data are collected from different molecular regulatory layers [for example: epigenomic, messenger RNA (mRNA), and proteomic data] using emerging high-throughput technologies.  ...  Similarly, Chen et al. 105 constructed a regulatory network in ES cells inferred from integrated data of transcription factor binding sites and expression profiles in undifferentiated and differentiated  ... 
doi:10.1002/wsbm.93 pmid:20890967 pmcid:PMC2951283 fatcat:g5z72rddurhldkjco5wcvkyaha

Relating protein adduction to gene expression changes: a systems approach

Bing Zhang, Zhiao Shi, Dexter T. Duncan, Naresh Prodduturi, Lawrence J. Marnett, Daniel C. Liebler
2011 Molecular Biosystems  
We developed a systems approach for relating protein adduction to gene expression changes through the integration of protein adduction, gene expression, protein-DNA interaction, and protein-protein interaction  ...  We demonstrated the general applicability of transcription factor-based signaling network inference using 103 known pathways.  ...  (NIEHS) through grants P30 ES000267 and P01 ES013125.  ... 
doi:10.1039/c1mb05014a pmid:21594272 pmcid:PMC3659419 fatcat:z2m3dqvmnnc7zgc6w3xm5iktze

BRNI: Modular analysis of transcriptional regulatory programs

Iftach Nachman, Aviv Regev
2009 BMC Bioinformatics  
We integrate the regulatory relations from the expression-and motif-based models into a single network, highlighting specific topologies that result in distinct dynamics of gene expression in the fission  ...  Previous methods allow dissecting regulatory modules from genomics data, such as expression profiles, protein-DNA binding, and promoter sequences.  ...  Acknowledgements We thank Nir Friedman for discussion, Ilan Wapinski for critical reading of the manuscript and Naomi Habib and Tommy Kaplan for assistance with the motif pipeline.  ... 
doi:10.1186/1471-2105-10-155 pmid:19457258 pmcid:PMC2694189 fatcat:5v7c2bcmqveqzkxzk7tt2bxkse

DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia

Chuhui Wang, Xueqing Zong, Fanjie Wu, Ricky Wai Tak Leung, Yaohua Hu, Jing Qin
2022 Frontiers in Molecular Biosciences  
By integrating and analyzing ChIP-seq, CLIP-seq, RNA-seq, and shRNA-seq data in K562 using binding and expression target analysis and Statistical Utility for RBP Functions, we discovered a two-layer regulatory  ...  To investigate the functional mechanism of DRBPs, we collected data from a variety of databases and literature and identified 118 DRBPs, which function as both transcription factors (TFs) and splicing  ...  ChIPBase ChIPBase, an integrated resource and platform for Zhou et al. (2017) High decoding transcription factor binding maps, expression profiles, and transcriptional regulation of long noncoding RNAs  ... 
doi:10.3389/fmolb.2022.920492 pmid:36052164 pmcid:PMC9425088 fatcat:jaq7j5lcdnctjjypte3zegdnaa

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

J. F. Moxley, M. C. Jewett, M. R. Antoniewicz, S. G. Villas-Boas, H. Alper, R. T. Wheeler, L. Tong, A. G. Hinnebusch, T. Ideker, J. Nielsen, G. Stephanopoulos
2009 Proceedings of the National Academy of Sciences of the United States of America  
Integrating system-wide measurements such as gene expression with networks of proteinprotein interactions and transcription factor binding revealed critical insights into cellular behavior.  ...  Although mRNA expression alone did not directly predict metabolic response, this correlation improved through incorporating a network-based model of amino acid biosynthesis (from r ‫؍‬ 0.07 to 0.80 for  ...  This work was supported by National Institutes of Health Grant 1R01 DK075850-01, the National Science Foundation International Research Fellowship Program, the Singapore-Massachusetts Institute of Technology  ... 
doi:10.1073/pnas.0811091106 pmid:19346491 pmcid:PMC2672541 fatcat:ynqb5ouarva3rdqpebvlowjm3m
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