(Q33298403)

25 July 2017

Orthologous transcription factors in bacteria have different functions and regulate different genes (English)

1 reference

25 July 2017

Adam P Arkin

3

0 references

author name string

Morgan N Price

series ordinal

1

1 reference

PubMed ID

17845071

25 July 2017

Paramvir S Dehal

series ordinal

2

1 reference

25 July 2017

1 September 2007

1 reference

PLOS Computational Biology

25 July 2017

1 reference

25 July 2017

3

1 reference

25 July 2017

1739-1750

1 reference

25 July 2017

9

1 reference

Creative Commons CC0 License

25 July 2017

start time

7 September 2007

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

1 reference

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RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

21 June 2018

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BadM is a transcriptional repressor and one of three regulators that control benzoyl coenzyme A reductase gene expression in Rhodopseudomonas palustris

21 June 2018

1 reference

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Bacterial regulatory networks are extremely flexible in evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The life-cycle of operons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Evolution of transcriptional regulatory networks in microbial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database

21 June 2018

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RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

21 June 2018

1 reference

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Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes

21 June 2018

1 reference

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Highways of gene sharing in prokaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The MicrobesOnline Web site for comparative genomics

21 June 2018

1 reference

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The net of life: reconstructing the microbial phylogenetic network

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Evolutionary origins of genomic repertoires in bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

A novel method for accurate operon predictions in all sequenced prokaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Making connections between novel transcription factors and their DNA motifs.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

NCBI GEO: mining millions of expression profiles--database and tools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Global transcriptome analysis of the heat shock response of Shewanella oneidensis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Nitrite-responsive activation of the nitrate assimilation operon in Cyanobacteria plays an essential role in up-regulation of nitrate assimilation activities under nitrate-limited growth conditions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

UniProt: the Universal Protein knowledgebase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The balance of driving forces during genome evolution in prokaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The Stanford Microarray Database: data access and quality assessment tools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Gene regulation in Lactococcus lactis: the gap between predicted and characterized regulators.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Network motifs in the transcriptional regulation network of Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Regulation of flagellar assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

SubtiList: the reference database for the Bacillus subtilis genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Identifying regulatory networks by combinatorial analysis of promoter elements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Polar flagellar motility of the Vibrionaceae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

On surrogate methods for detecting lateral gene transfer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Isolation and characterization of a Shewanella putrefaciens MR-1 electron transport regulator etrA mutant: reassessment of the role of EtrA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The COG database: new developments in phylogenetic classification of proteins from complete genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Homology a personal view on some of the problems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Cell-cycle control of a cloned chromosomal origin of replication from Caulobacter crescentus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Evolutionary dynamics of prokaryotic transcriptional regulatory networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Anaerobic regulation by an atypical Arc system in Shewanella oneidensis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

QuickTree: building huge Neighbour-Joining trees of protein sequences.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

The closest BLAST hit is often not the nearest neighbor.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1971122

Orthology: another terminology muddle

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17845071

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17845071

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.0030175

1 reference

journals/ploscb/PriceDA07

25 July 2017

1 reference

DBLP Dataset 2021-01-02

release_ja6dq64urbdeppfzlx3rxkvrnm

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ja6dq64urbdeppfzlx3rxkvrnm

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

1971122

1 reference

25 July 2017

1 reference

PubMed ID

17845071