nfi:Expression: Difference between revisions

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Fixing GBrowse image on Expression pages.
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*  
*  
****************************************************************************************** -->{{Help Cellular levels}}
****************************************************************************************** -->{{Help Cellular levels}}
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|- align='left' bgcolor='#CCCCFF'
|- align='left' bgcolor='#CCCCFF'
!|Molecule!!Organism or Strain!!Cellular level!!Units!!Medium!!Temperature °C!!Other (e.g. anaerobic)!!Growth rate!!Assay used!!Notes!!Reference(s)
!|Molecule!!Organism or Strain!!Value!!Units!!Experimental Conditions!!Assay used!!Notes!!Reference(s)
|-
|
Protein
|
Ecoli K-12
|
5.986+/-0.056
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
 
|
Single Molecule Fluorescence
|
PMID:20671182
|-
|
mRNA
|
Ecoli K-12
|
0.084947839
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
 
|
by RNA_Seq
|
PMID:20671182
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
169
|
molecules/cell/generation
|
*Medium: MOPS Complete 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
 
|
PMID: 24766808
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
229
|
molecules/cell/generation
|
*Medium: MOPS Minimal 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
 
|
PMID: 24766808
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
204
 
|
molecules/cell/generation
|
*Medium: MOPS Complete without Methionine 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
 
|
PMID: 24766808


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****************************************************************************************** -->{{expression_transcription_help}}
****************************************************************************************** -->{{expression_transcription_help}}
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!|Transcription unit(s)
!|Transcription unit(s)
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[[:Category:Txn_unit:nudC|nudC]]  
[[:Category:Txn_unit:nudC|nudC]]  


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==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
{{BacktoTop}}
{{BacktoTop}}
<protect>{{GBrowseFigureByCoord|4196793|4196833|ecoli|MG1655|Gene+DNA_+Protein|400|{{Nterm_closeup}} }}
<protect><gbrowseImage>
name=NC_000913:4196793..4196833
source=MG1655
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
{{Nterm_closeup}}
 
<!--Translation_notes--></protect>
<!--Translation_notes--></protect>
===Notes===
===Notes===
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*  
*  
****************************************************************************************** -->{{Expression_allele_table_help}}
****************************************************************************************** -->{{Expression_allele_table_help}}
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!|Allele Name!!Mutation!!Phenotype!!Reference
!|Allele Name!!Mutation!!Phenotype!!Reference


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****************************************************************************************** -->{{Expression_studies_table_help}}
****************************************************************************************** -->{{Expression_studies_table_help}}
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!|Type!!Reference!!Notes
!|Type!!Reference!!Notes
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|-  
|-  
|
|
microarray  
microarray
|
|
[http://genexpdb.ou.edu/index.php?query=b3998 GenExpDB:b3998] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://genexpdb.ou.edu/index.php?query=b3998 GenExpDB:b3998] ([[EcoliGenExpDB|EcoliWiki Page]])  
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Summary of data for nfi from multiple microarray studies   
Summary of data for nfi from multiple microarray studies   


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****************************************************************************************** -->{{Expression_resource_table_help}}
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!|Resource Name!!Resource Type!!Description!!Source!!Notes
!|Resource Name!!Resource Type!!Description!!Source!!Notes


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****************************************************************************************** -->{{Gene_accessions_help}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11915 EcoCyc:EG11915]
EcoCyc:EG11915
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1859 EchoBASE:EB1859]
EchoBASE:EB1859
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
EcoGene:EG11915
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001843
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11915 EcoGene:EG11915]
ASAP:ABE-0013068
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 19:19, 21 July 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Overview Transcription Translation Turnover Experimental Links References Suggestions

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

5.986+/-0.056

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182[1]

mRNA

Ecoli K-12

0.084947839

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182[1]

Protein

E. coli K-12 MG1655

169

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[2]

Protein

E. coli K-12 MG1655

229

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[2]

Protein

E. coli K-12 MG1655

204

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[2]

edit table

Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

nudC

edit table
Figure courtesy of RegulonDB


Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<gbrowseImage> name=NC_000913:4196793..4196833 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3998 (EcoliWiki Page)

NCBI GEO profiles for nfi

microarray

GenExpDB:b3998 (EcoliWiki Page)

Summary of data for nfi from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
edit table

<protect>

Notes

Accessions Related to nfi Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11915

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1859

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3998

EcoGene

EcoGene:EG11915

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001843

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013068

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 Taniguchi, Y et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329 533-8 PubMed
  2. ↑ 2.0 2.1 2.2 Li, GW et al. (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 624-35 PubMed

Categories

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