Table 2 Resources for gene regulation in E. coli K-12

RegulonDB

Transcriptional regulation, operons, regulons, gensor units

http://regulondb.ccg.unam.mx

Yes

[3]

EcoCyc

Regulation, transport, metabolism

https://ecocyc.org

Yes

[4]

COLOMBOS

Expression compendia of bacterial organisms

http://colombos.net

Yes

[1]

STRING

Protein-protein interaction network

http://string-db.org

Yes

[20]

GEO

Genomics HT data repository

https://www.ncbi.nlm.nih.gov/geo/

Yes

[21]

ArrayExpress

Repository of HT functional genomics experimental results

https://www.ebi.ac.uk/arrayexpress/

Yes

[22]

PortEco

Next-generation data for Escherichia coli

http://porteco.org

No

[5]

GenExpDB

Expression compendia

https://genexpdb.okstate.edu

No

–

EcoGene

E. coli K-12 genome and proteome information

http://ecogene.org

No

[23]

GenProtEC

Functions encoded by the Escherichia coli K-12 genome

http://genprotec.mbl.edu

No

[24]

EchoBASE

Information from postgenomic experiments

https://www.york.ac.uk/res/thomas/

No

[25]

Bacteriome

Integrates physical (protein-protein) and functional interactions

http://www.compsysbio.org/bacteriome/

–

[26]

EcoProDB

Integrates protein information

http://eecoli.kaist.ac.kr/main.html

–

[27]

M3D

Resource for microbial gene expression data

http://m3d.mssm.edu

No

[2]