ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage
ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization—from the genome to the ecosyste...
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| Format: | Article |
| Language: | en_US |
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Oxford University Press
2012
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| Online Access: | http://hdl.handle.net/1721.1/72444 |
| _version_ | 1826215863948148736 |
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| author | Kelly, Libusha Huang, Katherine H. Ding, Huiming Chisholm, Sallie (Penny) |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Kelly, Libusha Huang, Katherine H. Ding, Huiming Chisholm, Sallie (Penny) |
| author_sort | Kelly, Libusha |
| collection | MIT |
| description | ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization—from the genome to the ecosystem—embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light–dark cycle reveals the choreography of gene expression in cells in a ‘natural’ state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included. |
| first_indexed | 2024-09-23T16:38:14Z |
| format | Article |
| id | mit-1721.1/72444 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:38:14Z |
| publishDate | 2012 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/724442022-10-02T08:37:09Z ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage Kelly, Libusha Huang, Katherine H. Ding, Huiming Chisholm, Sallie (Penny) Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Chisholm, Sallie (Penny) Chisholm, Sallie (Penny) Kelly, Libusha Huang, Katherine H. Ding, Huiming ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization—from the genome to the ecosystem—embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light–dark cycle reveals the choreography of gene expression in cells in a ‘natural’ state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included. National Science Foundation (U.S.) (Center for Microbial Oceanography: Research and Education, grant OCE-0425602) National Science Foundation (U.S.) (Center for Microbial Oceanography: Research and Education, grant EF0424599) United States. Dept. of Energy (GTL grant number DE-FG02-02ER63445) United States. Dept. of Energy (GTL grant number DE-FG02-08ER64516) United States. Dept. of Energy (GTL grant number DE-FG02-07ER64506) Gordon and Betty Moore Foundation (Grant Award Letter #495.01) 2012-08-29T20:24:24Z 2012-08-29T20:24:24Z 2011-11 2011-10 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/72444 Kelly, L. et al. “ProPortal: a Resource for Integrated Systems Biology of Prochlorococcus and Its Phage.” Nucleic Acids Research 40.D1 (2011): D632–D640. Web. en_US http://dx.doi.org/10.1093/nar/gkr1022 Nucleic Acids Research Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/2.5 application/pdf Oxford University Press Oxford |
| spellingShingle | Kelly, Libusha Huang, Katherine H. Ding, Huiming Chisholm, Sallie (Penny) ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage |
| title | ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage |
| title_full | ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage |
| title_fullStr | ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage |
| title_full_unstemmed | ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage |
| title_short | ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage |
| title_sort | proportal a resource for integrated systems biology of prochlorococcus and its phage |
| url | http://hdl.handle.net/1721.1/72444 |
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