Database Overview: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Line 81: Line 81:


|-
|-
|gene name
| rowspan='3'|gene name
|experimental data
|experimental data
*gene expression
|-
*protein interaction
|
*gene expression
| [[ASAP]] (replace these)
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[GenoBase]]
Line 92: Line 93:
| Other
| Other
| Notes
| Notes
|-
|
*protein interaction
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|gene name (species 1)
|gene name (species 1)
Line 104: Line 116:


|-
|-
|gene name
| rowspan='3'|gene name
|*mutations
|
*mutations
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|
*sequence difference
*sequence difference
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|
*phenotype
*phenotype
| [[ASAP]] (replace these)
| [[ASAP]] (replace these)

Revision as of 17:09, 19 June 2006

Features at different databases

Query types

Query by gene name

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name (e.g. lacY) sequence description
 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes

function,localization,process (GO definitions )

 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes

gene name (namespace1)

gene name (namespace2)
Some namespaces:

  • genbank
 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • pdb
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • ecogene
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name pathway ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name experimental data
  • gene expression
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • protein interaction
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name (species 1) gene name( species 2) ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name
  • mutations
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • sequence difference
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • phenotype
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by pathway

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
pathway gene name ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
metabolic process *regulatory circuits ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
*transcription factors/sites ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by DNA location or sequence

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
DNA location Gene name ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
sequence related sequence (BLAST) ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by Function

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene function (GO term)

same for process and other GO branches

gene name ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by strain

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
strain ID *gene name ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
*mutation ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
*source ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&oldid=2237"