ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage
Name
Kelly-2011-ProPortal.pdf
Size
5.41 MB
Format
Adobe PDF
Checksum (MD5)
60e8d41c976f642cfbd8ae1ceaaf3e95
Author(s)
Kelly, Libusha
Huang, Katherine H.
Ding, Huiming
Chisholm, Sallie (Penny)
Date Issued
November 2011
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
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.
Version
Final published version
Abstract
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.
MIT Department
Massachusetts Institute of Technology. Department of Biology
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/nar/gkr1022
