Database Overview

Query types

Query by gene name

Query inputs and outputs

Input	Output	How this is handled in different databases
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,localization,process (GO definitions )	ASAP GenoBase EcoCyc EcoGene RegulonDB KEGG: (no result)
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
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
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

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
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

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

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

Query inputs and outputs

Input	Output	How this is handled in different databases
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)