Description

Gene co-expression plots

The co-expressing genes with each APOBEC3 gene are annotated, and the functional barcodes are shown for the selected cohort. Select the gene-set category to plot using the drop-down menu.

Genes were sorted, from left to right in descending order, by the correlation of their expression with that of the respective APOBEC3 gene.

Description

Distinguishing gene plot

We compared co-expression data in cancer/tissue types affected by APOBEC3 mutagenesis with those not affected, and extracted genes which show significant differences in the correlations. There were also subjected to functional barcoding.

Top: Scatterplot of the difference in median (DM):

DM = median(APOBEC-enriched cancer/tissue types) - median(others)

- APOBEC3-enriched cancer types are: BRCA, LUAD, LUSC, BLCA, CESC and HNSC (Roberts et al Nature Genetics , 2013). In this plot, one dot represent one gene. As shown the genes were ranked by this DM measure.

Below: functional barcodes. Each row represents one gene-set category:

- Innate: Innate immunity (Angelova et al Genome Biol , 2015)

- Adaptive: Adaptive immunity (Angelova et al Genome Biol , 2015)

- CC: Cell cycle (Fischer et al Nucleic Acids Res , 2016)

- DDR: DNA Damage Response (Pearl et al Nat Rev Cancer , 2015)

- LysAc: Lysine acetylation (Choudhary et al Science , 2009)

- SUMO: SUMOylation (Hendriks et al Nat Struct Mol Biol , 2014)