CyanoEXpress

What is CyanoEXpress?

CyanoEXpress is a user-friendly web-server, which enables interactive exploration of curated genome-wide expression data for the cyanobacterium Synechocystis sp. PCC 6803. CyanoEXpress is regularly updated with new data retrieved from public repositories: Gene Expression Omnibus, ArrayExpress and KEGG. Quality control, data pre-processing and normalization have been carried out to ensure the reliability of the data. Currently, CyanoEXpress comprises expression data from 753 microarray measurements carried out in 33 independent studies. Additionally, we have started to include publicly available RNA-Seq data. Notably, changes in expression during both environmental and genetic perturbations are included in the integrated data set. In total, CyanoEXpress includes over distinct 197 expression entries for 3078 Synechocystis protein-coding genes. For RNA-seq data, expression data for non-coding genes are also available.

CyanoEXpress is a project of the Systems Biology and Bioinformatics Laboratory at the University of Algarve and was created to assist researchers in the characterization and functional annotation of genes in cyanobacteria. The visualisation tool used on our web-server is based on a modified version of GeneXplorer application.

What are the applications of CyanoEXpress?

CyanoEXpress enables examination and visualisation of gene expression changes during experimental or genetic manipulation. Genes are clustered based on the similarity of the expression changes in order to facilitate the identification of coherent expression patterns of co-regulation across different conditions. For example, CyanoEXpress can be used to examine the transcriptional response of co-expressed genes to identify potential regulatory associations. Here, the user can determine under which environmental conditions or genetic perturbations, a co-expressed group of genes is up- or down-regulated. In this way, co-expression patterns can be used to identify common underlying regulatory mechanisms.

Furthermore, CyanoEXpress can be used to assign un-annotated genes to functions based on their coexpression with genes of known functions. This feature is advantageous given that numerous Synechocystis genes are yet to be assigned functions. For more focused investigations, sub-sets of expression data for specific cellular functions (i.e. Photosynthesis and respiration, Amino acid biosynthesis, Regulatory functions, Transcription, and Translation) are provided. Hence, the user can select a specific function and visualize the transcriptional response of the set of genes associated with that particular function across the full range of microarray measurements.

How can I use CyanoEXpress?

CyanoEXpress is easy and straight-forward to use. The first step is to choose an expression data set. Users can choose to access the full set of microarrays measurements, microarray measurements that only include measurements for environmental perturbations, or RNA-seq measurements. Alternatively, microarray-based gene expression data sets including only genes associated with specific functions, such as Translation can be selected.

The user then chooses the set of genes, whose expression changes will be displayed. This can be done either by selecting a gene cluster from a miniature heat map, or by inputting gene identifiers or names. Expression changes for each gene are colour-coded by a green to red colour gradient, corresponding to decreased (green) or increased (red) expression with respect to the control sample. No differences in expression are represented by black squares; while grey squares represent missing data for specific genes under that condition. The overall graphical view is given as a matrix formed by rows representing genes, and columns representing the microarray measurements. Finally, a simple mouse-click on a specific row generates a display of the genes, which show a high correlation with the gene corresponding to that particular row.

A more detailed overview of the functions available in CyanoEXpress can be found on the Help page. Or simply lean back and enjoy our video tutorial:




References for CyanoEXpress

Miguel Hernandez-Prieto and Matthias E. Futschik (2012) CyanoEXpress: a web database for interactive exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803, Bioinformation, 8 (13),634-638 (Abstract, Pdf)

Miguel HernŠndez-Prieto , Trudi Semeniuk , Joaquin Giner-Lamia and Matthias Futschik (2016) The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803, Scientific Reports 6:22168 (pdf + html)

CyanoEXpress was supported through the PTDC/BIA-MIC/101036/2008 and PTDC/BIA-MIC/4418/2012 grants. by the FundaÁăo para a CiÍnca e a Technologia.