H2A.Z localization patterns in bladder cancer cells. (A) Average chromatin immunoprecipitation (ChIP) enrichment signals are shown over regions spanning 10 kb around the transcription start sites (TSSs) of all the human genes from UCSC Refseq database. Green and red lines indicate the level of H2A.Z enrichment in normal UROtsa and cancer LD611 cells, respectively. (B) Tag density plots display H2A.Z distribution relative to the TSS. Several representative peaks specific for LD611 and UROtsa cells were also shown. Each horizontal line represents an individual gene, and the enrichment values for H2A.Z are illustrated by color density. (C) H2A.Z-enriched genes in LD611 cells were classified into four distinct groups based on false discovery rate (FDR) and the level of locus-specific chromatin state (NLCS) density. Groups 1 and 2 show NLCS ratio ≥8.5 and 8 to 8.5 with FDR ≤0.01 and FDR ≤0.05, respectively. Group 3 has FDR ≤0.05 with NLCS level from 7.5 to 8.5. Group 4 has FDR ≥0.05 with NLCS ≤8. (D) H2A.Z-enriched genes in LD611 cells were subjected to ingenuity pathway analysis. Seven top biological functions including bladder cancer signaling were identified with a threshold set at P = 0.05.