Objectives: Functional characterization of genes selected from variant discovery experiments in retina dystrophy.

Whole exome sequencing (WES) is useful in de novo variant discovery. After analyze some patients, we get a group of genes with some characterized mutations and through functional enrichment we get additional information that allows improve the understanding of that process they regulate.

Data: 73 genes with variants of subjects with retina dystrophy. File: dystrophy.txt

Workflow:

1. Open the file “dystrophy.txt” in a text editor and inspect its content. How many genes are there?
2. Upload the file in Babelomics through the Upload button. We have to specify the data type: “Id list (Id)”.
3. Select the functional enrichment analysis tool in the menu “Functional / Single Enrichment: FatiGO”.
4. Firstly, we compare our list against the rest of genome. We have to select our data and organism (human).
5. It's possible perform simultaneously several enrichment analysis using different databases. In this exercise, we select biological process, molecular functions and cellular components from Gene Ontology.
6. We name the job and execute the task. It may expend about 20 minutes in complete the job.

Questions:

1. How many GO terms are significant? (Biological process, molecular functions and cellular components)
2. How many terms are significant using FDR < 0.005 as threshold?
3. We are interested in term “cellular response to light stimulus(GO:0071482)” (biological process). In our list, which genes are enriched with that function?
4. What means sign and value of logarithm of Odds Ratio?
5. How do we interpret the graphic that appears under the significant results?