Michael P. Schroeder and Abel Gonzalez-Perez
This year our lab will participate again in the Gulbenkian Training Program in Bioinformatics (GTPB). Abel and Michael will give a 3 days course on Bioinformatics for Integrative Genomics – BIG12, from 7th to 9th May. The course is now open for Inscriptions, and a tentative program can be found here.
GTPB program is very well known for its practical courses on bioinformatics, which have been running since 1999. The courses are eminently practical, including few lectures and many hands on exercises. The groups are small, usually up to 20 attendees, which allows a very intense experience with the topic, the instructors and the rest of attendees.
BIG12 course will focus on the analysis of multidimensional and heterogeneous data in biomedical genomics. The use of microarray and next generation sequencing technologies yields complex, multidimensional data sets that describe in detail the myriad of changes that occur within individual cells in complex diseases such as cancer, and how these changes differ between patients, cells or conditions. Bioinformatic skills are required to analyse this data and extract useful knowledge out of it. The course will address questions like: Which of the long list of mutations detected are likely to affect the function of the protein and which ones are probably neutral?; Which of the genes affected by those mutations are already known to be involved in cancer or other diseases?; Which pathways or biological processes are affected by the transcriptomic alterations detected in my experiment? How can we integrate diverse data types from a cohort of patients (including clinical data, transcriptomic data, mutations etc.)?
The course will teach how to answer these questions using bioinformatics approaches. In particular we will extensively use three tools developed in our lab: IntOGen, Gitools and Condel.
Some of the topics that will be addressed are describe in the following posts. Take a look at them and if you’re interested come join us in the course!
Exploring multiple cancer genomics alterations with Gitools
Visualizing mutually exclusive alteration patterns in cancer with Gitools
Exploring the effect of cancer genomic alteration on expression with Gitools
Sample Level Enrichment Analysis (SLEA) in Gitools to assess the transcriptional status of pathways per tumor
Three questions you can answer with IntOGen
IntOGen Biomart portal
Condel in the world of web services
The making of Condel (CONsensus DELeteriousness Score)
Basic and intuitive analysis of microarray datasets using Gitools (Part 1)
Basic and intuitive analysis of microarray datasets using Gitools (Part 2)