ProPortal

A resource for integrated systems biology of Prochlorococcus and its phage

Libusha Kelly, Katherine H. Huang, Huiming Ding, Sallie W. Chisholm

Research output: Contribution to journalArticle

24 Citations (Scopus)

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.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume40
Issue numberD1
DOIs
StatePublished - Jan 2012
Externally publishedYes

Fingerprint

Prochlorococcus
Systems Biology
Bacteriophages
Synechococcus
Genome
Metagenomics
Ecosystem
Ecotype
Gene Expression
Photoperiod
Cyanobacteria
Multigene Family
Transcriptome
Oceans and Seas
Population
Genes
Down-Regulation
Databases

ASJC Scopus subject areas

  • Genetics

Cite this

ProPortal : A resource for integrated systems biology of Prochlorococcus and its phage. / Kelly, Libusha; Huang, Katherine H.; Ding, Huiming; Chisholm, Sallie W.

In: Nucleic Acids Research, Vol. 40, No. D1, 01.2012.

Research output: Contribution to journalArticle

Kelly, Libusha ; Huang, Katherine H. ; Ding, Huiming ; Chisholm, Sallie W. / ProPortal : A resource for integrated systems biology of Prochlorococcus and its phage. In: Nucleic Acids Research. 2012 ; Vol. 40, No. D1.
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