EcoliWiki - User contributions [en]

Database Overview

2006-06-21T19:46:18Z

YiJu: /* Query by gene name */

[[Category:Databases]]
=Content & Features at different databases=

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (linked to COG)
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to GenBank)
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to PDB)
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (Linked to EcoGene)
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to CGSC)
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

Database Overview

2006-06-21T19:42:59Z

YiJu:

[[Category:Databases]]
=Content & Features at different databases=

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

Database Overview

2006-06-21T19:33:17Z

YiJu:

[[Category:Databases]]
=Content & Features at different databases=

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

Database Overview

2006-06-21T19:24:19Z

YiJu:

[[Category:Databases]]
=Content & Features at different databases=

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]
*[[EcoCyc]]
*[[EcoGene]]
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}