-5 October 2016 -
CyanoEXpress 2.3: Additional information about integrated studies included
In the new version of CyanoEXpress, we included more detailed information about the treatment and control conditions in the integrated transcriptome studies. The information is also provided in the supplementary data of our recent Scientific Reports publication. We also modified the appearance and structure of the Sample Information page. We hope that these new features will help users of CyanoEXpress in the interpretation of results from the interactive analyses.
-28 April 2016 -
In memory of Hans Matthijis The expression data used to create CyanoEXpress has given us the opportunity to collaborate with many researchers using expression microarrays for Synechocystis. One of those was Dr. Hans Matthijs, who was always very supportive of our project. Hans saw it as a great tool for cyanobacterial research. His many contributions to the study of gene expression in cyanobacteria have led to a more in depth understanding of the photosynthetic process, as well as to mitigation of the effects of toxic cyanobacteria in lakes (for more details, see his ResearchGate page). In addition to these great scientific achievements, we were always happy to meet with Hans and he always greeted us with a smile. It was common to see him surrounded by PhD students, or engaged in deep discussion with other researchers at scientific meetings. His last e-mail to some of his closer collaborators reflected his interest in the human side of science; he didn't want to leave without saying goodbye, and made sure his students would be well looked after.
Thank you, Hans, for your great contribution to science and our scientific community. For sure, that at the next meeting on cyanobacteria, we will turn to look for you in spirit, every time someone laughs.
-29 February 2016 -
Publication presenting systems analyses based on CyanoEXpress
Today, our analyses of the Synechosystis transcriptome integrated in CyanoEXpress was published in Scientific Reports. In this study, we used the collected data to elucidate the transcriptional regulation of photosynthesis and its coordination with other processes. Furthermore, we illustrate how data from CyanoEXpress can be used to identify novel genes connected to the photosynethesis apparatus in Synechocystis.
- 2 January 2016 -
New Synechocystis microarray datasets included
We added several new microarray studies for Synechocystis, that were published in GEO - GSE59371 (6 microarrays), GSE59451 (13 microarrays), GSE50060 (13 microarrays), GSE69981 (3 microarrays) to CyanoExpress. Additionally, we set up a page Data processing, which outlines the data processing steps carried for CyanoExpress.
- 16 November 2015 -
Video tutorial for CyanoEXpress!!!
Finally, we managed to make a short video tutorial outlining the main features of CyanoEXpress. We hope you enjoy it.
- 2 August 2015 -
CyanoExpress version 2.0: Now with RNA-Seq data included!
CyanoEXpress takes a leap forward and includes now RNA-Seq data. For a start, we incorporated the RNA-Seq data from the study by Kopf et al., in which gene expression of 10 different conditions were profiled by RNA-Seq. Notably, this data set comprises expression data not only for protein coding genes on the chromosome, but also protein-coding genes on the plasmids and non-coding genes. To be consistent with the current layout of CyanoEXpress, which presents expression changes compared to controls, the RNA-Seq data are shown as logged fold changes compared to exponentially growing Synechocystis under normal conditions. This also corresponds to the experimental design of the study, as 9 different conditions were induced after transferring exponentially growing cultures. Thus, the new RNA-Seq dataset includes fold changes with respect to exponential growth for 9 different conditions such as cold stress, heat stress, Fe limitation. Note that the work by Kopf et al. primarily assigns expression to transcriptional units. To still enable listing by genes, we assumed the same expression for genes belonging to the same transcriptional unit.
Further RNA-Seq data will be included in the future. So stay tuned ;-)
- 20 April 2015 -
CyanoEXpress version 1.7: Query of multiple genes
In the new version of CyanoEXpress, it is possible to query for multiple genes using either their gene symbols or, preferably, their gene ids. This enables the comparison of the transcriptional regulation of two or more genes. An example, in which we query and visualize the expression changes of all genes in the isiA operon, can be found in the updated help pages.
- 3 November 2014 -
CyanoEXpress version 1.6: Inclusion of all main functional categories
We have now included expression matrices for all main functional categories as defined in Cyanobase with exception of the categories for "Unknown", "Hypothetical" and "RNA" genes.
- 23 July 2014 -
CyanoEXpress version 1.5: New order of samples in gene expression matrices & color coding
We have re-arranged the order of the samples, so that measurements of similar environmental perturbations are adjacent in the expression matrix. For instance, all experiments measuring the transcriptional response to changes of light quality and intensity are now next to each other. Also, the naming of the sample labels is now more consistent. All samples with wild-type have labels starting with "WT", while mutants start with the gene symbols of the (usually) deleted gene. In the combined expression matrix, the samples from mutants are arranged together with the WT based on environmental perturbation applied except mutants profiled under standard conditions, which are placed on the far right side. Furthermore, an additional color scheme for samples was introduced. Color bars below the listed samples indicate similar type of perturbation or stress. In the gene expression set integrating measurements for wild type and mutants, a further thinner color bar helps to distinguish between wild type and mutant. We hope these changes will facilitate the inspection of the transcriptional patterns.
Please note that in some cases the changes might not show up in the displayed heatmaps. You may notice that the displayed fold changes do not correspond to the displayed colors. For instance, the heatmap shows green color for an expression level, despite positive log fold changes. In this cases, the frames have to be explicitly reloaded and if persisting, the images stored in the browser cache need to be removed. For the latter, you simply need to delete the browser cache.
- 25 November 2013 -
CyanoEXpress version 1.4: New datasets included
CyanoEXpress continues to assist cyanobiologists in their quest to identify new regulatory relationships. The expression data has been revised to incorporate three new datasets generated with two different Agilent platforms used by the CyanoLab in Freiburg and by Prof. Hans Matthijs in the University of Amsterdam. These new datasets correspond to circadian-like experiments (PMID: 23601192), Copper depletion (GSE41411), and low carbon acclimation (PMID: 22096149). The inclusion of these datasets strengthens the capacity of CyanoEXpress to serve as an exploratory tool or to confirm gene relationships observed in the wet lab.
- 20 November 2013 -
CyanoEXpress meets CyanoFactory
CyanoEXpress traveled to Porto in November 2013, where the new datasets and recent work from the SysBioLab were well received by members of the CyanoFactory consortia.
- 8 July 2013 -
CyanoEXpress version 1.3: Additional normalization of circadian data
An additional normalization step was used for data from the experiment by Kucho et al. 2005 (PMID: 15743968) measuring gene expression under circadian oscillations. Here, the expression values were adjusted for each gene individually, so that the mean expression over the full day-night cycle is equal zero. This is to facilitate the inspection of differential expression observed in the experiment. For instance, positive expression values signify that the gene is higher expressed at this time point of the day-night cycle compared to its average expression.
- 20 April 2013 -
CyanoEXpress presented in Pultusk, Poland
Matthias gave an overview of CyanoExpress at the ESF-EMBO Symposium during his talk "How the internal world of Synechocystis adapts to the ever-changing world outside: A comprehensive meta-analysis of its transcriptional response". Best of all: Even in a fresh, blue shirt - thanks to his generous room-mate Vicente Rubio! (His own luggage got lost on the trip to Poland.)
- 23 January 2013 -
CyanoEXpress at the ESF Research Conference
CyanoExpress will be presented at the ESF-EMBO Symposium "Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment" which will take place in Pultusk, Poland from 15th to 20th April 2013. See you there!
- 4 September 2012 -
Release of CyanoEXpress Version 1.2
CyanoEXpress includes now abbreviated gene names (such as isiA) besides the official gene index (e.g.sll0247) and the definition in Cyanobase (e.g. 'iron-stress chlorophyll-binding protein, homologous to psbC'). These abbreviations can be also used for search.
- 7 August 2012 -
CyanoEXpress presented at the ISPP 2012, Porto
We presented CyanoExpress at the 14th International Symposium on Phototrophic Prokaryotes in Porto, Portugal. The poster presenting CyanoEXpress can be found (here). We would like thank again for the great interest!!
- 1 August 2012 -
Release of CyanoEXpress Version 1.1
In the newly released version of CyanoEXpress, a enhanced interface is provided for the examination of the displayed expression profiles. Using the pointer, gene and sample names as well as logged fold changes are simultaneously shown in the top frame of the CyanoEXpress web application.
- 6 July 2012 -
CyanoEXpress Publication in Bioinformation
The CyanoEXpress database, its features and implementation are described in the new issue of Bioinformation (Abstract+Pdf).
- 31 May 2012 -
Release of CyanoEXpress Version 1.0
The first version of CyanoEXpress has become publicly accessible. It provides access to Synechocystis expression data collected in over 30 individual studies. The integrated web application allows interactive inspection of co-expression patterns.