Visualizing mutually exclusive alteration patterns in cancer with Gitools

By |2023-11-08T09:54:31+00:00March 8th, 2012|Categories: BioinfoTips|Tags: , , , , , , , |

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. [...]

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Sample Level Enrichment Analysis (SLEA) in Gitools to assess the transcriptional status of pathways per tumor

By |2023-11-08T09:54:31+00:00February 21st, 2012|Categories: BioinfoTips, Uncategorized|Tags: , |

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 [...]

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Understanding the hierarchy of your GO Terms subset

By |2023-11-08T09:54:32+00:00April 7th, 2011|Categories: BioinfoTips|Tags: , , , , |

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.

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Basic and intuitive analysis of microarray datasets using Gitools (Part 1)

By |2023-11-08T09:54:32+00:00March 16th, 2011|Categories: BioinfoTips|Tags: , , , , , , |

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. [...]

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Visualized ChIP & ChIPseq protocol

By |2023-11-08T09:54:32+00:00January 25th, 2011|Categories: BioinfoTips|Tags: , , |

[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 [...]

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