##Correlate (enrichment) B2 SINE position to mRNA isoform difference ###If we can figure this out? ###B2 position to expression - isoform and gene level ##Comparison of how many genes are DE in Brf1 KD vs. Ctrl Inf. and how many have B2 in them? ##How many genes have B2s in them in the genome? ##How many genes are induced during infection contain a B2 SINE? ###Highlight based on B2 SINE position in gene ###Volcano plot ##How many genes are induced during infection in a Pol3-dependent manner? ###Ctrl inf vs Ctrl mock ###Brf1 vs Ctrl inf. ###Bar graph to display this data ###At isoform level too - use all mRNA isoforms % as reference ##Look at the background distribution of B2 SINEs and compare it to our empirical data ##Is there a stop codon in the mRNA isoforms with retained introns? ##Send Azra isoform usage data w/ B2 location and gene ##GO term with DE isoforms with a B2 ##Average size of B2 SINE? ###Intact B2 = ~180bp ##Distance analyses? ###Eg. distance of B2 SINE from nearest exon and its effect on mRNA isoform