EcoCyc
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| Link/URL: | |
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| What: |
Comprehensive database of E. coli molecular components |
| Who: |
Peter Karp, SRI |
| Updates: |
Every 3 months |
| Upcoming events: | |
| Web Services: |
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| edit table |
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Contents
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 databases at SRI International in Menlo Park, CA.
Content
- Genes
- Name and synonyms
- Nucleotide position and sequence
- Paralogs
- Proteins and RNAs
- Name and synonyms
- Minireview summary
- Enzyme activators, inhibitors, cofactors, reaction catalyzed, alternative substrates
- Subunit structure, molecular weight, pI, amino acid sequence
- Metabolites
- Metabolic reactions, transport reactions
- Metabolic pathways
- Regulatory network
- Regulation by transcription factors, attenuators, small RNAs
- Promoters, transcription factor binding sites, terminators
- Operons (transcription units)
- Regulatory interactions
Using EcoCyc
Browsing
Tools
- Omics viewers: Paint omics datasets onto the full metabolic map, the full genome, or the transcriptional regulatory network (desktop mode only)
- Interactive interrogation and tracing through metabolic network (desktop mode only)
- Interactive interrogation of regulatory network (desktop mode only)
- Genome map browser
- Comparative genome map browser
- Comparative operations for genomics and metabolism
Searching
The main EcoCyc searches are based on a three-tiered search mechanism:
- Quick search: Enter a phrase into the quick-search box and type Enter. The phrase can be a complete or partial gene name, protein name, metabolite name, pathway name, or Gene Ontology term.
- The second tier of searching allows more elaborate object-specific searches, under the Search menu. For example, Search->Gene/Proteins/RNAs allows you to formulate searches that filter based on gene or protein name, sequence length, molecular weight, cellular location, etc.
- The third tier of searching involves complex searches against multiple object types, and are typically used for global analysis of E. coli. See Search->Advanced.
Other searches under the Search menu include ontology-based searching and searches against the full text of E. coli articles available in EcoCyc.
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. Note that EcoCyc-authored minireviews and citations are found on the protein page, not the gene page. Example gene page: http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10686
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 MapsTM, 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" button that is half way down the gene page. 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.
Online Help
[Web seminars on how to use EcoCyc.]
[Guided tour of different EcoCyc Web page types.]
Usage examples
These papers cite EcoCyc papers 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. [Full text in PNAS]
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. [Full text in PNAS]
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. [Full text in PLoS]
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.[Full text in NAR]
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.[Full text in NAR]
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.[Full text in NAR]
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. [Full text in NAR]
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. [Full text in NAR]
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. [Full text in NAR]
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. [Full text in NAR]
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. [Full text in BMC Bioinformatics]
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. [Full text in BMC Bioinformatics]
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. [Full text in BMC Bioinformatics]
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. [Full text in NAR]
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. [Full text in NAR]
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. [Full text in AEM]
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. [Full text in Genome Research]
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. [Full text in Plant Phys]
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. [Full text in NAR]
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. [Full text in NAR]
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. [Full text in NAR]
Technology
EcoCyc runs in two modes. The desktop mode that you install locally on a Macintosh, PC, or Linux box is faster and has more extensive features than the Web version, and is what most heavy users employ. The web server mode provides information via the Internet. More information on these modes: EcoCyc Modes
The Pathway Tools software behind EcoCyc is written in Common Lisp. Pathway Tools has been applied to hundreds of other genomes, within BioCyc and by groups outside SRI.
Web Services/API
Programming interfaces in Lisp, Perl, and Java are described here.
Discussion
References
See Help:References for how to manage references in EcoliWiki.
I.M. Keseler et al, EcoCyc: A comprehensive view of Escherichia coli biology, Nucleic Acids Research 37:D464-70 2009. [Article text]
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.
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.
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.
