November 25: One-day training activity
From raw matrices to differential expression/methylation patterns: a functional genomics approach to detect molecular insights
Luca Ambrosino, Francesco Cecere
CNR – Institute of Genetics and Biophysics Adriano Buzzati-Traverso, Naples, Italy
This training activity will show to the participants some bioinformatics methods to analyze raw data matrices from transcriptomics/epigenomics experiments. In details, some techniques of normalization and visualization of expression data, together with a procedure of identification of Differentially Expressed Genes (DEGs), will be shown. Moreover, a functional enrichment analysis will be performed on the dataset of the detected DEGs, to discover biological functions that are over-represented in a particular condition with respect to a reference background, obtaining insights about the molecular mechanisms and biological processes that are associated with the experimental condition under study.
Similarly, steps will be performed to analyze methylation data, starting from the methylation value of each single CpG site in the experiment, leading to the identification of the Differentially Methylated Probes (DMPs). Together, these biological information will help to understand relationships between gene regulation mechanisms and environmental/external factors.
Participants need a laptop with R (https://www.r-project.org/) and Ontologizer (http://ontologizer.de/) software installed.
In particular, the following R packages should be installed:
– DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
– Pheatmap (https://rdrr.io/cran/pheatmap/)
– Stringr (https://cran.r-project.org/web/packages/stringr/readme/README.html)
– Ggplot2 (https://ggplot2.tidyverse.org/)
– Corrplot (https://www.rdocumentation.org/packages/corrplot/versions/0.94)
– Gplots (https://www.rdocumentation.org/packages/gplots/versions/3.2.0)
– ChAMP (https://bioconductor.org/packages/release/bioc/html/ChAMP.html)
How to register: after the registration to the Conference, you will receive information to attend the workshop (no additional cost). The number of participants is limited, if you are interested please contact as soon as possible the Conference organization.