Gene Expression Analysis Tools

Publications.

GETools web software

Huerta A.M., Glasner J.D., Richmond C.S., Blattner F.R., Moreno-Hagelsieb G., and Collado-Vide J. "Biological Congruence of Global Expression Profiles in Escherichia coli" (submitted in Genome Biology).
Huerta A.M., Glasner J.D., Hongfan J., Blattner F.R., Gutiérrez-Ríos R.M., and Collado-Vides J. (2002) "GETools (version 1): Gene Expression Tool for Analysis of Transcriptome Experiments in Escherichia coli." TIGS 18:217-218. (PDF).

E.coli K12

Escherichia Coli

Computational Predictions
The details of the methods used for these predictions are published in a couple of papers:

Thieffry D.; Salgado H.; Huerta A.M., and Collado-Vides J. (1998) "Prediction of transcription regulatory sites in the complete genome of Escherichia coli" Bioinformatics 14 (5): 391-400.

Pérez-Rueda E., and Collado-Vides J. (2000) "The Repertoire of DNA-Binding Transcriptional Regulators in Escherichia coli" Nucleic Acids Research 28:1838-1847.

Salgado H., Moreno-Hagelsieb G., Smith T.F., and Collado-Vides J. "Operons in Escherichia coli: Genomic analyses and predictions", Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 12, 6652-6657, June 6, 2000.

Benítez-Bellón E., Moreno-Hagelsieb G. and Collado-Vides J. (2002) "Evolution thresholds to detect regulatory DNA-binding sites: An evaluation by the use of data on experimentally characterized regulons" Genome Biology 3:(3): 13.1-13.16

http://www.ccg.unam.mx/Computational_Genomics/PromoterTools/

Data Base
The information on the database used for these predictions is contained in RegulonDB, -see

http://regulondb.ccg.unam.mx/

and the associated publications:

Huerta A.M.; Salgado H.; Thieffry D. y Collado-Vides J. (1998) "RegulonDB: A Database on Transcription Regulation in Escherichia coli" Nucleic Acids Res. 26:55-60.

Salgado H.; Santos A.; Garza-Ramos U.; van Helden J.; Díaz E.; and Collado-Vides J. (1999). "RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli" Nucleic Acids Research. 27(1): 59-60.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Millán-Zárate D., Blattner F.R., and Collado-Vides J. (2000) "RegulonDB (version 3.0): Transcriptional Regulation and Operon Organization in Escherichia coli" Nucleic Acids Research 28: 65-67.

Salgado H., Gama-Castro S., Martínez-Antonio A., Díaz-Peredo E., Sánchez- Solano F., Peralta-Gil M., Garcia-Alonso D., Jiménez-Jacinto V., Santos-Zavaleta A., Bonavides-Martínez C., and Collado-Vides J.(2004) "RegulonDB (version 4.0): Transcriptional Regulation, Operon Organization and Growth Conditions in Escherichia coli K-12", Nucleic Acids Research 32: 303-306.

Salgado H., Gama-Castro S., Peralta-Gil M., Díaz-Peredo E., Sánchez-Solano F., Santos-Zavaleta A., Martínez Flores I., Jiménez-Jacinto V., Bonavides-Martínez C., Segura-Salazar J., Martínez-Antonio A. , and Collado-Vides J. "RegulonDB (version 5.0): Escherichia coli K-12 Transcriptional Regulatory Network, Operon Organization, and Growth Conditions" (2006) Nucleic Acids Res. Vol(34):394-397.