The ability of the retinoblastoma protein (pRB) to restrict the cell cycle is well known. Since KDM5A/RBP2/JARID1A is associated with pRB/E2F, one may wonder about its recruitment and its role in the cell cycle. In our study we determined how KDM5A uses its demethylating capability on cell cycle genes during differentiation. We also wanted to know if the demethylation function of KDM5A is non-redundant. It was previously shown that KDM5A and E2F colocalize. We aimed to know at what point of the cell cycle KDM5A is recruited, and whether E2F plays a role in KDM5A recruitment or vice-versa. We focused on the genomic localization of KDM5A in mouse ES cells and human U937 cells at different stages of development.
We have been preparing a new version of Gitools with many improvements, amongst which there is a new IGV search, the use of categorical scales and new data aggregation methods that can be used to annotate the heatmap.
Gitools is an interactive heatmap viewer which can also perform various analysis over the data. Heatmaps in Gitools can be multidimensional, with various values per cell, which is very practical for cancer genomics data analysis and visualization (read more).
Let us introduce the new features step by step.
We are proud to share with you the Beta version of IntOGen V.04 at http://beta.intogen.org. This new version includes many changes both in content and in layout. In this post I will summarize the main novelties and in following posts we will give more details of the new version.
Several weeks ago we realized we were having problems retrieving the functional impact scores from the MutationAssessor webservice into our condel web server. We immediately corrected the problem by setting up a proxy in our server; nevertheless, we don’t have a clear idea of how long this problem may have been going on. A little later, we discovered that apparently condel scores computed through our web server may have been malformed due to a mismanagement of the response the server obtained from the MutationAssessor webserver. (Note that this problem only affects condel scores computed through the web server, not via the PERL standalone script.)