Database Overview

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 *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 sequence difference 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