Research visit at IMPPC

I visited the cancer research institute IMPPC and conducted research in the area of bioinformatics under supervision of Roberto Malinverni and Marcus Buschbeck.

I supported the team on the development of the R-package “regioneR” for evaluating significance of overlaps between genomic region sets in a biologically reasonable way. Furthermore I clustered transcription-related factors, such as transcription factors, histone modifications or DNase, based on the regions of the genome that they occupy. I compared this clustering with the cell line characteristics karyotype, lineage, tissue and sex in order to evaluate if common characteristics form clusters. The resulting clusters suggest that region sets with the same lineage, karyotype and sex have slightly more overlaps in genomic regions whereas for the tissue such correlation cannot be observed.

cluster-cells-interactions-characteristics1
Hierarchical clusters of cell lines based on the overlaps of their genomic region sets and indication of lineage, tissue, karyotype and sex of the cell lines in the heatmap.