APOBEC3 functional barcodes

applet to display APOBEC3 gene annotation data. Copyright Joseph Ng 2018. Please cite:
Ng JCF, Quist J, Grigoriadis A, Malim MH & Fraternali F. 'Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases'. Nucleic Acids Research 47(3):1178-1194, 2019.

How to use

Here gene co-expression analysis of human APOBEC3 genes in different cancer/tissue cohorts are visualised. We extracted genes in 2 types of analyses and functionally annotate them, generating 'functional barcodes' to show these annotations.

  1. gene co-expression : genes whose expression are correlated with that of each APOBEC3 gene.
  2. distinguishing genes : from (1), extracting those genes which show differential correlations in those cancer/tissue types reportedly affected by APOBEC3 mutagenesis, compared to those sites which are not affected.

Users can visualise the plots interactively and download the underlying data tables for more detailed analyses.

Users can also study functional barcodes based on more fine-grained gene sets, for example, gene set signature specific to CD8+ T cells. Select under 'Specific Gene Sets' when you select the gene set to plot in the drop-down menu.

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)