Visualizing mutually exclusive alteration patterns in cancer with Gitools
On the quest to identify cancer driver genes, it has been observed that driver alterations that affect a pathway tend to be altered in a mutually exclusive manner. [...]
Exploring multiple cancer genomics alterations with Gitools.
Cancer genomics data that is produced creates multi-dimensional data sets. Gitools lets you browse all that data at once. A typical cancer genomics project nowadays [...]
Sample Level Enrichment Analysis (SLEA) in Gitools to assess the transcriptional status of pathways per tumor
The identification of molecular biomarkers from expression data is a major objective in cancer research. It is clear that there is a benefit in pathway [...]
SVGMap: Configurable image browser for experimental data
Have you ever heard of SVG? Scalable Vector Graphics (SVG) is an open standard to design images and graphics that can be scaled to any size without [...]
Understanding the hierarchy of your GO Terms subset
The other day I downloaded the cancer-affected Gene Ontology (GO) terms from IntOGen for up- and down-regulation via it's Biomart interface for a few tissues. Since was only interested in the GO Cell Compartment terms, so I directly added a filter file containing all the GO CC Terms as a filter for the Biomart export. So then... what do you do when you have a list of GO terms? Already if it is only 100 GO terms, it is quite hard to get an idea which are the affected compartments. To understand better you have to identify the more general terms that are affected. Here I explain quickly how I solved this problem and share it with you.
Basic and intuitive analysis of microarray datasets using Gitools (Part 2)
In this series of posts I am showing how expression data can be analyzed using Gitools. In a previous post I explained how to do pathway enrichment [...]
Basic and intuitive analysis of microarray datasets using Gitools (Part 1)
After preparing some tutorials for our software, I thought it would be useful to show how basic analyses on microarray data can be carried out using Gitools. [...]
Visualized ChIP & ChIPseq protocol
[hana-flv-player video=”http://bg.upf.edu/blog/videos/JoVE_2101_Benevolenskaya.flv” width=”400″ height=”330″ description=”” player=”4″ autoload=”true” autoplay=”false” loop=”false” autorewind=”true” /] ChIP-seq (Chromatin Immunoprecipitation-and-Sequencing) has become a popular technique to find de novo and genome-wide binding sites [...]
Three questions you can answer with IntOGen
1. Do you have a favorite gene? Would you like to know if it is altered in cancer samples in any way (e.g. mutated, amplified, downregulated)? [...]
