Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor (Q36328910)

13 August 2017

Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor (English)

1 reference

13 August 2017

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Streptomyces coelicolor

object named as

Streptomyces coelicolor

1 reference

5

George Karypis

1 reference

13 August 2017

Salim Charaniya

1

1 reference

13 August 2017

Sarika Mehra

2

1 reference

13 August 2017

Wei Lian

3

1 reference

13 August 2017

Karthik P Jayapal

4

1 reference

13 August 2017

Wei-Shou Hu

6

1 reference

13 August 2017

language of work or name

English

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publication date

24 October 2007

1 reference

13 August 2017

Nucleic Acids Research

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13 August 2017

35

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13 August 2017

21

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13 August 2017

7222-7236

1 reference

The life-cycle of operons

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Analysis of gene expression in operons of Streptomyces coelicolor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Operon information improves gene expression estimation for cDNA microarrays

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Rho-dependent transcription termination: more questions than answers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Nur, a nickel-responsive regulator of the Fur family, regulates superoxide dismutases and nickel transport in Streptomyces coelicolor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A framework to analyze multiple time series data: a case study with Streptomyces coelicolor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A novel method for accurate operon predictions in all sequenced prokaryotes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Organization and expression of the polynucleotide phosphorylase gene (pnp) of Streptomyces: Processing of pnp transcripts in Streptomyces antibioticus

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Predicting bacterial transcription units using sequence and expression data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Computational identification of operons in microbial genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Co-expression pattern from DNA microarray experiments as a tool for operon prediction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Conserved economics of transcription termination in eubacteria

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Prediction of operons in microbial genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Support vector machine classification and validation of cancer tissue samples using microarray expression data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Transcriptional and mutational analyses of the Streptomyces lividans recX gene and its interference with RecA activity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Operons in Escherichia coli: genomic analyses and predictions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Knowledge-based analysis of microarray gene expression data by using support vector machines

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

The use of gene clusters to infer functional coupling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Genetic manipulation of antibiotic-producing Streptomyces

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Growth phase-dependent transcription of the Streptomyces ramocissimus tuf1 gene occurs from two promoters

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2).

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Functions of the gene products of Escherichia coli.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A computer algorithm for testing potential prokaryotic terminators

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Two promoters, one inducible and one constitutive, control transcription of the Streptomyces lividans galactose operon

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Cloning and characterization of the histidine biosynthetic gene cluster of Streptomyces coelicolor A3(2).

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Genome-wide operon prediction in Staphylococcus aureus

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

DevA, a GntR-like transcriptional regulator required for development in Streptomyces coelicolor.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Light-induced carotenogenesis in Streptomyces coelicolor A3(2): identification of an extracytoplasmic function sigma factor that directs photodependent transcription of the carotenoid biosynthesis gene cluster

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Prediction of transcription terminators in bacterial genomes.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

The expression of the trpD, trpC and trpBA genes of Streptomyces coelicolor A3(2) is regulated by growth rate and growth phase but not by feedback repression

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Phylogenetic Analysis of Streptomyces spp. Causing Potato Scab Based on 16S rRNA Sequences

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

An operon for histidine biosynthesis in Streptomyces coelicolor. I. Genetic evidence.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Coenzyme B12 controls transcription of the Streptomyces class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

The absB gene encodes a double strand-specific endoribonuclease that cleaves the read-through transcript of the rpsO-pnp operon in Streptomyces coelicolor

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Regional organization of gene expression in Streptomyces coelicolor

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Operon prediction without a training set.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Is cross-validation valid for small-sample microarray classification?

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Negative feedback regulation of dnaK, clpB and lon expression by the DnaK chaperone machine in Streptomyces coelicolor, identified by transcriptome and in vivo DnaK-depletion analysis.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A Bayesian network approach to operon prediction

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Two transcriptional regulators GlnR and GlnRII are involved in regulation of nitrogen metabolism in Streptomyces coelicolor A3(2).

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A powerful non-homology method for the prediction of operons in prokaryotes

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

SigB, an RNA polymerase sigma factor required for osmoprotection and proper differentiation of Streptomyces coelicolor.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Use of contiguity on the chromosome to predict functional coupling.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Engineering support vector machine kernels that recognize translation initiation sites

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

A probabilistic learning approach to whole-genome operon prediction.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Identification and transcriptional characterization of the gene encoding the stress-response sigma factor sigma(H) in streptomyces coelicolor A3(2).

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Operon prediction based on SVM

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Stress-response sigma factor σ Η is essential for morphological differentiation of Streptomyces coelicolor A3(2)

21 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2175336

Activity of the Streptomyces coelicolor stress-response sigma factor sigmaH is regulated by an anti-sigma factor

5 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17959654

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17959654

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identification of sigmaB-dependent promoters using consensus-directed search of Streptomyces coelicolor genome

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17959654

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKM501

1 reference

13 August 2017

1 reference

13 August 2017

PubMed publication ID

17959654

1 reference