Evidence map›Paper›PMID 25632108›Full record

ArticleDatabase : the journal of biological databases and curation2015

CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.

Yaohua Yang, Jie Feng, Tao Li, Feng Ge, Jindong Zhao

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

  1. Review
  2. Review
  3. Molecular glue for phycobilisome attachment to photosystem II inProceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  4. Article
  5. Article
  6. Article
  7. Observational
  8. Article
  9. Review
  10. Article
  11. Engineering the fatty acid synthesis pathway inBiotechnology for biofuels · 2018
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Yaohua YangKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China.
Jie FengKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China.
Tao LiKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China litao@ihb.ac.cn gefeng@ihb.ac.cn.
Feng GeKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China litao@ihb.ac.cn gefeng@ihb.ac.cn.
Jindong ZhaoKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, University of Chinese Academy of Sciences, Beijing 100049, China, College of Life Science, Peking University, Beijing 100871, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

Databases, GeneticGene Expression ProfilingProteomicsSynechococcusTranscriptome

Identifiers

PMID25632108
PMCPMC4309022

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.