Kulak, Dept. Development and Regeneration
Vergelijkende transcriptoomanalyse van de mens met andere diersoorten (voor banaba)
Op basis van informatie bekomen uit genoombrowsers en analyse van big data bestanden (bijvoorbeeld genbank files) worden genen en hun transcripten met elkaar vergeleken van zowel mens als verschillende diersoorten. Dit levert informatie op over de functie van genen, ontwikkeling van organismen en evolutie. Toegepaste technieken zijn textmining, databases manipuleren en aanmaken, sequentieanalyse en visualisatietechnieken.
Abstract traineeship advanced bachelor of bioinformatics 2017-2018: Comparative transcriptomic analysis between species
During the internship, in the KuLeuven of Kortijk, several projects, that were given by the mentor, were handled by the intern. The first one was the processing and comparison of expression data between data of 2 articles and the data given by a laboratory in Leuven. For this several normalizations were tested before an actual PCA could be done. As for the visualization, there were also numerous packages that were tested to produce 3D plots and to see if they had the ability to export it as a vector (pdf or svg).
In the following assignment, the intern also had to find a way as to how they would visualize the differences between dendrograms created from the hierarchical clustering of species based on GC content, GC landscapes and the tree of life. For this the package dendextend was used to create tanglegrams, which puts two dendrograms next to each other and draws lines to the corresponding species. An entanglement factor was also calculated, this represent the degree of difference between the two dendrograms as a number.
Etienne Sabbelaan 53
Prof. dr. ir. Lieven Thorrez
+32 (0) 56 24 62 31