Defining bacterial regulons using ChIP-seq
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1250945
- Grant/Contract Number:
- FC02-07ER64494
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Methods
- Additional Journal Information:
- Journal Name: Methods Journal Volume: 86 Journal Issue: C; Journal ID: ISSN 1046-2023
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Myers, Kevin S., Park, Dan M., Beauchene, Nicole A., and Kiley, Patricia J. Defining bacterial regulons using ChIP-seq. United States: N. p., 2015.
Web. doi:10.1016/j.ymeth.2015.05.022.
Myers, Kevin S., Park, Dan M., Beauchene, Nicole A., & Kiley, Patricia J. Defining bacterial regulons using ChIP-seq. United States. https://doi.org/10.1016/j.ymeth.2015.05.022
Myers, Kevin S., Park, Dan M., Beauchene, Nicole A., and Kiley, Patricia J. Tue .
"Defining bacterial regulons using ChIP-seq". United States. https://doi.org/10.1016/j.ymeth.2015.05.022.
@article{osti_1250945,
title = {Defining bacterial regulons using ChIP-seq},
author = {Myers, Kevin S. and Park, Dan M. and Beauchene, Nicole A. and Kiley, Patricia J.},
abstractNote = {},
doi = {10.1016/j.ymeth.2015.05.022},
journal = {Methods},
number = C,
volume = 86,
place = {United States},
year = {Tue Sep 01 00:00:00 EDT 2015},
month = {Tue Sep 01 00:00:00 EDT 2015}
}
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https://doi.org/10.1016/j.ymeth.2015.05.022
https://doi.org/10.1016/j.ymeth.2015.05.022
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Works referenced in this record:
Mapping E. coli RNA Polymerase and Associated Transcription Factors and Identifying Promoters Genome-Wide
book, January 2011
- Davis, Sarah E.; Mooney, Rachel A.; Kanin, Elenita I.
- Methods in Enzymology
The regulation of bacterial transcription initiation
journal, January 2004
- Browning, Douglas F.; Busby, Stephen J. W.
- Nature Reviews Microbiology, Vol. 2, Issue 1
Widespread suppression of intragenic transcription initiation by H-NS
journal, January 2014
- Singh, S. S.; Singh, N.; Bonocora, R. P.
- Genes & Development, Vol. 28, Issue 3
Model-based Analysis of ChIP-Seq (MACS)
journal, January 2008
- Zhang, Yong; Liu, Tao; Meyer, Clifford A.
- Genome Biology, Vol. 9, Issue 9
ChIP-Seq and RNA-Seq Reveal an AmrZ-Mediated Mechanism for Cyclic di-GMP Synthesis and Biofilm Development by Pseudomonas aeruginosa
journal, March 2014
- Jones, Christopher J.; Newsom, David; Kelly, Benjamin
- PLoS Pathogens, Vol. 10, Issue 3
MEME-ChIP: motif analysis of large DNA datasets
journal, April 2011
- Machanick, Philip; Bailey, Timothy L.
- Bioinformatics, Vol. 27, Issue 12
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12
journal, December 2011
- Prieto, Ana I.; Kahramanoglou, Christina; Ali, Ruhi M.
- Nucleic Acids Research, Vol. 40, Issue 8
The DNA-binding network of Mycobacterium tuberculosi s
journal, January 2015
- Minch, Kyle J.; Rustad, Tige R.; Peterson, Eliza J. R.
- Nature Communications, Vol. 6, Issue 1
MEME: discovering and analyzing DNA and protein sequence motifs
journal, July 2006
- Bailey, T. L.; Williams, N.; Misleh, C.
- Nucleic Acids Research, Vol. 34, Issue Web Server
RSAT 2011: regulatory sequence analysis tools
journal, June 2011
- Thomas-Chollier, M.; Defrance, M.; Medina-Rivera, A.
- Nucleic Acids Research, Vol. 39, Issue suppl
Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009
- Li, H.; Durbin, R.
- Bioinformatics, Vol. 25, Issue 14
Activating Transcription in Bacteria
journal, October 2012
- Lee, David J.; Minchin, Stephen D.; Busby, Stephen J. W.
- Annual Review of Microbiology, Vol. 66, Issue 1
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000
- Kanehisa, Minoru; Goto, Susumu
- Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013
- Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
- Nucleic Acids Research, Vol. 42, Issue D1
An integrated software system for analyzing ChIP-chip and ChIP-seq data
journal, November 2008
- Ji, Hongkai; Jiang, Hui; Ma, Wenxiu
- Nature Biotechnology, Vol. 26, Issue 11
ChIP-Seq for Genome-Scale Analysis of Bacterial DNA-Binding Proteins
book, January 2015
- Bonocora, Richard P.; Wade, Joseph T.
- Methods in Molecular Biology
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
EcoCyc: a comprehensive database of Escherichia coli biology
journal, November 2010
- Keseler, I. M.; Collado-Vides, J.; Santos-Zavaleta, A.
- Nucleic Acids Research, Vol. 39, Issue Database
EcoGene 3.0
journal, November 2012
- Zhou, Jindan; Rudd, Kenneth E.
- Nucleic Acids Research, Vol. 41, Issue D1
Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
journal, August 2009
- Neuweger, Heiko; Persicke, Marcus; Albaum, Stefan P.
- BMC Systems Biology, Vol. 3, Issue 1
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli
journal, May 1998
- Thieffry, Denis; Huerta, Araceli M.; Pérez-Rueda, Ernesto
- BioEssays, Vol. 20, Issue 5
WikiPathways: Pathway Editing for the People
journal, July 2008
- Pico, Alexander R.; Kelder, Thomas; van Iersel, Martijn P.
- PLoS Biology, Vol. 6, Issue 7
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
journal, November 2010
- Kahramanoglou, Christina; Seshasayee, Aswin S. N.; Prieto, Ana I.
- Nucleic Acids Research, Vol. 39, Issue 6
Transcription Factor Binding Site Mapping Using ChIP-Seq
journal, April 2014
- Jaini, Suma; Lyubetskaya, Anna; Gomes, Antonio
- Microbiology Spectrum, Vol. 2, Issue 2
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
journal, July 2010
- Wilbanks, Elizabeth G.; Facciotti, Marc T.
- PLoS ONE, Vol. 5, Issue 7
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools
journal, November 2013
- Hu, James C.; Sherlock, Gavin; Siegele, Deborah A.
- Nucleic Acids Research, Vol. 42, Issue D1
Inferring direct DNA binding from ChIP-seq
journal, May 2012
- Bailey, Timothy L.; Machanick, Philip
- Nucleic Acids Research, Vol. 40, Issue 17
Identification of HilD-Regulated Genes in Salmonella enterica Serovar Typhimurium
journal, December 2013
- Petrone, B. L.; Stringer, A. M.; Wade, J. T.
- Journal of Bacteriology, Vol. 196, Issue 5
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
journal, August 2009
- Defrance, Matthieu; van Helden, Jacques
- Bioinformatics, Vol. 25, Issue 20
Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding
journal, June 2013
- Myers, Kevin S.; Yan, Huihuang; Ong, Irene M.
- PLoS Genetics, Vol. 9, Issue 6
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
journal, January 2010
- Goecks, Jeremy; Nekrutenko, Anton; Taylor, James
- Genome Biology, Vol. 11, Issue 8
Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators
journal, June 2014
- Fumeaux, Coralie; Radhakrishnan, Sunish Kumar; Ardissone, Silvia
- Nature Communications, Vol. 5, Issue 1
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
journal, July 1999
- Hertz, G. Z.; Stormo, G. D.
- Bioinformatics, Vol. 15, Issue 7
dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
journal, October 2013
- Chung, Dongjun; Park, Dan; Myers, Kevin
- PLoS Computational Biology, Vol. 9, Issue 10
Normalization of ChIP-seq data with control
journal, August 2012
- Liang, Kun; Keleş, Sündüz
- BMC Bioinformatics, Vol. 13, Issue 1
The Mycobacterium tuberculosis regulatory network and hypoxia
journal, July 2013
- Galagan, James E.; Minch, Kyle; Peterson, Matthew
- Nature, Vol. 499, Issue 7457
The Human Genome Browser at UCSC
journal, May 2002
- Kent, W. J.; Sugnet, C. W.; Furey, T. S.
- Genome Research, Vol. 12, Issue 6
A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
journal, January 2009
- Lun, Desmond S.; Sherrid, Ashley; Weiner, Brian
- Genome Biology, Vol. 10, Issue 12
MEME SUITE: tools for motif discovery and searching
journal, May 2009
- Bailey, T. L.; Boden, M.; Buske, F. A.
- Nucleic Acids Research, Vol. 37, Issue Web Server
Characterization of the RpoN regulon reveals differential regulation of T6SS and new flagellar operons in Vibrio cholerae O37 strain V52
journal, June 2012
- Dong, Tao G.; Mekalanos, John J.
- Nucleic Acids Research, Vol. 40, Issue 16
JBrowse: A next-generation genome browser
journal, July 2009
- Skinner, M. E.; Uzilov, A. V.; Stein, L. D.
- Genome Research, Vol. 19, Issue 9
ChIP–seq: advantages and challenges of a maturing technology
journal, September 2009
- Park, Peter J.
- Nature Reviews Genetics, Vol. 10, Issue 10
The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
journal, May 2014
- Solans, Luis; Gonzalo-Asensio, Jesús; Sala, Claudia
- PLoS Pathogens, Vol. 10, Issue 5
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
journal, August 2008
- Valouev, Anton; Johnson, David S.; Sundquist, Andreas
- Nature Methods, Vol. 5, Issue 9
The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally
journal, October 2013
- Park, Dan M.; Akhtar, Md. Sohail; Ansari, Aseem Z.
- PLoS Genetics, Vol. 9, Issue 10
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
journal, September 2014
- Seo, Sang Woo; Kim, Donghyuk; Latif, Haythem
- Nature Communications, Vol. 5, Issue 1
Nitrogen stress response and stringent response are coupled in Escherichia coli
journal, June 2014
- Brown, Daniel R.; Barton, Geraint; Pan, Zhensheng
- Nature Communications, Vol. 5, Issue 1
Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling
journal, August 2012
- Kim, Donghyuk; Hong, Jay Sung-Joong; Qiu, Yu
- PLoS Genetics, Vol. 8, Issue 8
Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network
journal, October 2014
- Fitzgerald, Devon M.; Bonocora, Richard P.; Wade, Joseph T.
- PLoS Genetics, Vol. 10, Issue 10
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
journal, August 2012
- Guo, Yuchun; Mahony, Shaun; Gifford, David K.
- PLoS Computational Biology, Vol. 8, Issue 8
Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation
journal, July 2011
- Davies, B. W.; Bogard, R. W.; Mekalanos, J. J.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 30
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
journal, May 2002
- Dahlquist, Kam D.; Salomonis, Nathan; Vranizan, Karen
- Nature Genetics, Vol. 31, Issue 1
Quantifying similarity between motifs
journal, January 2007
- Gupta, Shobhit; Stamatoyannopoulos, John A.; Bailey, Timothy L.
- Genome Biology, Vol. 8, Issue 2
Transfer activation of SXT/R391 integrative and conjugative elements: unraveling the SetCD regulon
journal, February 2015
- Poulin-Laprade, Dominic; Matteau, Dominick; Jacques, Pierre-Étienne
- Nucleic Acids Research, Vol. 43, Issue 4
PICS: Probabilistic Inference for ChIP-seq
journal, June 2010
- Zhang, Xuekui; Robertson, Gordon; Krzywinski, Martin
- Biometrics, Vol. 67, Issue 1
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli
journal, March 2015
- Cho, Suhyung; Cho, Yoo-Bok; Kang, Taek Jin
- Nucleic Acids Research, Vol. 43, Issue 6
The Molecular Basis for Control of ETEC Enterotoxin Expression in Response to Environment and Host
journal, January 2015
- Haycocks, James R. J.; Sharma, Prateek; Stringer, Anne M.
- PLoS Pathogens, Vol. 11, Issue 1
Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
journal, April 2014
- Bonhoure, N.; Bounova, G.; Bernasconi, D.
- Genome Research, Vol. 24, Issue 7
Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein
journal, March 2012
- Blasco, Benjamin; Chen, Jeffrey M.; Hartkoorn, Ruben
- PLoS Pathogens, Vol. 8, Issue 3
Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing
journal, July 2014
- Conway, Tyrrell; Creecy, James P.; Maddox, Scott M.
- mBio, Vol. 5, Issue 4
Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon
journal, November 2013
- Stringer, A. M.; Currenti, S.; Bonocora, R. P.
- Journal of Bacteriology, Vol. 196, Issue 3
MochiView: versatile software for genome browsing and DNA motif analysis
journal, April 2010
- Homann, Oliver R.; Johnson, Alexander D.
- BMC Biology, Vol. 8, Issue 1
PathVisio 3: An Extendable Pathway Analysis Toolbox
journal, February 2015
- Kutmon, Martina; van Iersel, Martijn P.; Bohler, Anwesha
- PLOS Computational Biology, Vol. 11, Issue 2
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013
- Caspi, Ron; Altman, Tomer; Billington, Richard
- Nucleic Acids Research, Vol. 42, Issue D1
Detecting differential binding of transcription factors with ChIP-seq
journal, November 2011
- Liang, Kun; Keleş, Sündüz
- Bioinformatics, Vol. 28, Issue 1
ChIP ‐seq and transcriptome analysis of the OmpR regulon of S almonella enterica serovars T yphi and T yphimurium reveals accessory genes implicated in host colonization
journal, December 2012
- Perkins, Timothy T.; Davies, Mark R.; Klemm, Elizabeth J.
- Molecular Microbiology, Vol. 87, Issue 3
Global Analysis of Photosynthesis Transcriptional Regulatory Networks
journal, December 2014
- Imam, Saheed; Noguera, Daniel R.; Donohue, Timothy J.
- PLoS Genetics, Vol. 10, Issue 12
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination
journal, October 2014
- Carraro, Nicolas; Matteau, Dominick; Luo, Peng
- PLoS Genetics, Vol. 10, Issue 10
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
journal, July 2014
- Gomes, Antonio L. C.; Abeel, Thomas; Peterson, Matthew
- Genome Research, Vol. 24, Issue 10
The Generic Genome Browser: A Building Block for a Model Organism System Database
journal, October 2002
- Stein, L. D.
- Genome Research, Vol. 12, Issue 10
DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria
journal, May 2013
- Fioravanti, Antonella; Fumeaux, Coralie; Mohapatra, Saswat S.
- PLoS Genetics, Vol. 9, Issue 5