EcoCyc

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EcoCyc
Who:	Peter Karp, SRI
What:	Comprehensive database of E. coli' molecular components
Where:	EcoCyc
Updates	Every 3 months
Upcoming events	link to event calendar, if applicable
Web Services

About EcoCyc

EcoCyc is a database of literature-based "gold standard" annotation of the molecular components of E. coli K-12, primarily referencing strain MG1655. EcoCyc is a central part of the BioCyc collection of database at SRI International in Menlo Park, CA.

Content

Genes, Proteins, Compounds, and everything related. All possible types of pathways

Reactions:

 Binding 
 DNA repair
 EC 
 Protein-Ligand
 Reactions of Two Component Regulators
 Transport Reactions 
 Unclassified Reaction

Any possible type of Compound

Metabolic chart

 you can actually paint omics data onto the diagram

Omics Viewer

Using EcoCyc

Searching

When the input is a gene or protein:

This db tells you practically everything you ever wanted to know about a gene or protein. When you insert the query, the output allows a decision between the gene or its protein product. Most of the information is in the form of links. In fact, 90% of the page is link-able, which could get messy if you don't quite know what you are looking for. The information in EcoCyc is also specifically referenced, with the bibliography at the bottom of the linked page.
query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)

To get you started, here are a few things people generally want.

To get a sequence to enter into your Cloning software:

If you need the gene (start to stop codons) or protein sequence, click on the appropriate tab at the very top of the page. There is also a page that allows you to specify what range of DNA you want. To get back to the parC page, click the Back button of your browser. Very simple.

To see what genes flank your gene of interest:

Click on the genome browser link at the map position heading (4th heading down the page). You may see what flanks your gene as well as directionality. This tool resembles Google Maps^TM, in that it has arrows that allow you to move along the gene map in either direction. To get back to the previous page, just click the Back button of your browser.

To see where the gene is w.r.t. other organisms:

Click on the "Align in Multiple-Genome Browser" tab. Next select the organisms you want to compare (the alphabetical list goes across), select "submit" and there it is. If at any time you want to change or add organisms to the alignment process, click on the "select allowed organisms" tab at the top of the page, and you are free to change your preferences. You may also change the gene you are looking at from this page as well- up at the top.

Usage examples

Add links to additional pages describing success stories here.

These are other papers that cite the first paper listed in the reference section below. You could look at these for other examples of how this database is used.

The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons
Víctor González, Rosa I. Santamaría, Patricia Bustos, Ismael Hernández-González, Arturo Medrano-Soto, Gabriel Moreno-Hagelsieb, Sarath Chandra Janga, Miguel A. Ramírez, Verónica Jiménez-Jacinto, Julio Collado-Vides, and Guillermo Dávila Proc Natl Acad Sci U S A. 2006 March 7; 103(10): 3834–3839. Published online 2006 February 27. doi: 10.1073/pnas.0508502103.

Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach Swaine L. Chen, Chia-Seui Hung, Jian Xu, Christopher S. Reigstad, Vincent Magrini, Aniko Sabo, Darin Blasiar, Tamberlyn Bieri, Rekha R. Meyer, Philip Ozersky, Jon R. Armstrong, Robert S. Fulton, J. Phillip Latreille, John Spieth, Thomas M. Hooton, Elaine R. Mardis, Scott J. Hultgren, and Jeffrey I. Gordon Proc Natl Acad Sci U S A. 2006 April 11; 103(15): 5977–5982. Published online 2006 April 3. doi: 10.1073/pnas.0600938103.

Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters Dongying Wu, Sean C Daugherty, Susan E Van Aken, Grace H Pai, Kisha L Watkins, Hoda Khouri, Luke J Tallon, Jennifer M Zaborsky, Helen E Dunbar, Phat L Tran, Nancy A Moran, and Jonathan A Eisen PLoS Biol. 2006 June; 4(6): e188. Published online 2006 June 6. doi: 10.1371/journal.pbio.0040188.

Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner Nucleic Acids Res. 2006; 34(1): 1–9. Published online 2006 January 5. doi: 10.1093/nar/gkj405.

NPInter: the noncoding RNAs and protein related biomacromolecules interaction database Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, and Runsheng Chen Nucleic Acids Res. 2006 January 1; 34(Database issue): D150–D152. Published online 2005 December 28. doi: 10.1093/nar/gkj025.

MODOMICS: a database of RNA modification pathways Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, and Janusz M. Bujnicki Nucleic Acids Res. 2006 January 1; 34(Database issue): D145–D149. Published online 2005 December 28. doi: 10.1093/nar/gkj084.

PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways Natalia Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza Nucleic Acids Res. 2006 January 1; 34(Database issue): D369–D372. Published online 2005 December 28. doi: 10.1093/nar/gkj095.

MetaCyc: a multiorganism database of metabolic pathways and enzymes Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp Nucleic Acids Res. 2006 January 1; 34(Database issue): D511–D516. Published online 2005 December 28. doi: 10.1093/nar/gkj128.

The UCSC Archaeal Genome Browser Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M. Lowe Nucleic Acids Res. 2006 January 1; 34(Database issue): D407–D410. Published online 2005 December 28. doi: 10.1093/nar/gkj134.

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, and Julio Collado-Vides Nucleic Acids Res. 2006 January 1; 34(Database issue): D394–D397. Published online 2005 December 28. doi: 10.1093/nar/gkj156.

The comprehensive updated regulatory network of Escherichia coli K-12 Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp, and Julio Collado-Vides BMC Bioinformatics. 2006; 7: 5. Published online 2006 January 6. doi: 10.1186/1471-2105-7-5.

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, and Roland Eils BMC Bioinformatics. 2006; 7: 119. Published online 2006 March 8. doi: 10.1186/1471-2105-7-119.

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, and Masaru Tomita BMC Bioinformatics. 2006; 7: 168. Published online 2006 March 23. doi: 10.1186/1471-2105-7-168.

Detecting uber-operons in prokaryotic genomes Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, and Ying Xu Nucleic Acids Res. 2006; 34(8): 2418–2427. Published online 2006 May 8. doi: 10.1093/nar/gkl294.

Structure and function of negative feedback loops at the interface of genetic and metabolic networks Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, and Kim Sneppen Nucleic Acids Res. 2006; 34(8): 2455–2462. Published online 2006 May 9. doi: 10.1093/nar/gkl140.

In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments Bas Teusink, Frank H. J. van Enckevort, Christof Francke, Anne Wiersma, Arno Wegkamp, Eddy J. Smid, and Roland J. Siezen Appl Environ Microbiol. 2005 November; 71(11): 7253–7262. doi: 10.1128/AEM.71.11.7253-7262.2005.

Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states Stephen S. Fong, Andrew R. Joyce, and Bernhard Ø. Palsson Genome Res. 2005 October; 15(10): 1365–1372. doi: 10.1101/gr.3832305.

MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research Peifen Zhang, Hartmut Foerster, Christophe P. Tissier, Lukas Mueller, Suzanne Paley, Peter D. Karp, and Seung Y. Rhee Plant Physiol. 2005 May; 138(1): 27–37. doi: 10.1104/pp.105.060376.

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers M. L. Green and P. D. Karp Nucleic Acids Res. 2005; 33(13): 4035–4039. Published online 2005 July 20. doi: 10.1093/nar/gki711.

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor Nucleic Acids Res. 2005; 33(13): 4096–4105. Published online 2005 July 26. doi: 10.1093/nar/gki715.

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas Nucleic Acids Res. 2005; 33(19): 6083–6089. Published online 2005 October 24. doi: 10.1093/nar/gki892.

References

I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp. EcoCyc: A comprehensive database resource for Escherichia coli, Nucleic Acids Research 33:D334-7 2005.

See Also

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L., Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 Nucleic Acids Research 34:1-9 2006.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J., The comprehensive updated regulatory network of Escherichia coli K-12 BMC Bioinformatics 7:5 2006.

Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., and Saier M.H. Jr., The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database ASM News 70(1):25-30 2004.

External Links

EcoCyc