Chromatin Landscapes of Retroviral and Transposon Integration Profiles
A) Gene alignment plots showing the distribution of integrations across genes from 5 kb upstream to the transcription start site (TSS), transcription termination site (TTS), and 5 kb downstream. The red line depicts the integrations with sense orientation relative to the gene, blue depicts antisense. B) Biases with respect to genes for the unselected integration datasets. We distinguish between integrations within genes (genic), within 1 kb upstream of the TSS (TSS_upstream), within 1 kb downstream of the TSS (TSS_downstream), and other integrations (other). On the left, the color scale blue-gray-red represents increasing numbers of integrations, relative to expected. On the right, the color scale blue-gray-red represents the integration orientation bias relative to genes, from antisense to sense. Associations that are not significant (binomial test; FDR-corrected ) are white. C) Biases with respect to transcripts, distinguishing between integrations in 5′UTRs, 3′UTRs, exons and introns.