CyanOmics: An integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002
Open accessAbstract
Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present CyanOmics, a database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for systematic and comprehensive analysis of all those data. Powerful browsing and searching tools are integrated to help users directly access information of interest with enhanced visualization of the analytical results. Furthermore, Blast is included for sequence-based similarity searching and Cluster 3.0, as well as the R hclust function is provided for cluster analyses, to increase CyanOmics's usefulness. To the best of our knowledge, it is the first integrated omics analysis database for cyanobacteria. This database should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp. PCC 7002 and other cyanobacteria. Additionally, the entire database framework is applicable to any sequenced prokaryotic genome and could be applied to other integrated omics analysis projects. Database URL: http://lag.ihb.ac.cn/cyanomics.
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The genome of Synechococcus sp. PCC 7002 comprises one chromosome of approximately 3.0 Mb and six plasmids-pAQ1, pAQ3, pAQ4, pAQ5, pAQ6 and pAQ7-with plasmid sizes of approximately 4.8, 16, 32, 39, 124 and 186 kb, respectively.
“Its genome comprises one chromosome of approximately 3.0 Mb and six plasmids—pAQ1, pAQ3, pAQ4, pAQ5, pAQ6 and pAQ7—with plasmid sizes of approximately 4.8, 16, 32, 39, 124 and 186 kb, respectively [67].”
From Cyanobacteria as a Photosynthetic Chassis for Metabolic Pathway Engineering with Heterologous Gene Expression (2026) · cites this paper as [67]
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- Authors
- Yang, Y., Feng, J., Li, T., Ge, F., & Zhao, J.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Li, Tao
- Ge, Feng
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-01-01
- Volume
- 2015
- ISSN
- 1758-0463 (ISSN-L)
- PMC
- PMC4309022
- OpenAlex
- W2127619970
- Cited by
- 24
- References
- 32
- Citations by year
- 2026: 2 · 2025: 2 · 2023: 2 · 2022: 4 · 2021: 5 · 2020: 2 · 2019: 1 · 2018: 3 · 2017: 1 · 2016: 2
- FWCI
- 0.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Database (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Institute of Hydrobiology, CAS Institutional Repository (submittedVersion)
- Funders
- National Natural Science Foundation of China (31000113)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
- Keywords
- Synechococcus sp. PCC 7002, cyanobacteria, transcriptomics, proteomics, genome annotation, transcriptional patterns, proteomic profiling, sequence similarity searching, clustering
- MeSH terms
- Gene Expression Profiling, Databases, Genetic, Proteomics, Synechococcus, Transcriptome
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