I am pleased to share with you a 60” video animation explaining our IntOGen project using easy to understand terms:
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A video animation explains IntOGen in 60 seconds
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Finding correlated genes on TCGA expression data.
We have published a new section in IntOGen in collaboration with Hautaniemi Lab, where you can do a gene correlation with the gene expression results of TCGA (The Cancer Genome Atlas) for a given subset of patients that share some specific clinical annotations. Then you will be able to browse your correlations next to global gene expression, SNP survival and DNA methylation analyses. The data analyzed so far includes 4 tumor types from TCGA: glioblastoma multiforme (GBM; 507 samples), ovarian serous adenocarcinoma (OV; 546 samples), breast invasive carcinoma (BRCA; 525 samples) and colon adenocarcinoma (COAD; 161 samples).
Bioinformatics for Integrative Genomics course
We are pleased to announce that we will be giving another practical course on bioinformatics for Integrative Genomics this year. It will take place from November 7-9, 2011, in Oeiras, Portugal, as part of the Gulbenkian Training Programme in Bioinformatics. The course teachers will be Alba Jené and myself from our group. Read the rest of this entry »
IntOGen Biomart portal
The DATABASE Oxford Journal has published a new volume in September dedicated to Biomart related databases and tools.
We have had a Biomart portal for IntOGen data since 2010 and we were invited to write a manuscript describing it. Read the rest of this entry »
Version 3 of IntOGen!
We have worked hard during the last months to release the new version of IntOGen, version 03, which we have published today. We are very proud of this new release, as it includes some major improvements. Read the rest of this entry »
Browsing ICGC data in IntOGen
When we created IntOGen we had the motivation to convert it into a discovery tool for cancer researchers and a resource that integrates multidimensional OncoGenomics Data. We have now made a new important step in IntOGen project: we have included all somatic mutations detected by the International Cancer Genome Consortium (ICGC) projects. Read the rest of this entry »
BG is giving a course on Bioinformatics for Integrative Genomics
On 21-22 June our group is organizing a course open to all reserachers who share our interest on Genomics. It will be similar to the one we gave at the Gulbenkian Institute last november, but this time we will not be focusing on Cancer Genomics but on Genomics in general, so that we can satisfy a broader audience of scientists. Read the rest of this entry »
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? Read the rest of this entry »
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 analysis. Here I explain how to identify genes significantly up-regulated in a cancer dataset using Oncodrive. Read the rest of this entry »
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)? Read the rest of this entry »