EcoCyc: Difference between revisions
| Line 62: | Line 62: | ||
''Add links to additional pages describing success stories here.'' | ''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. | |||
=Other sites with related content= | =Other sites with related content= | ||
Revision as of 23:08, 27 June 2006
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.
| 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
Browsing
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 referenced, with the bibliography at the bottom of the linked page.
query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)
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.
Technology
Web Services/API
Discussion
Trackbacks
This feature is not yet functional
- $4$5: [$2 $1]
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.