Integrative analysis with complex biological meanings. (A) Integrative analysis pipeline for RNA-Seq data based and several attached optional sequencing applications with biological meanings. (B) Genome data could be integrated with transcriptome data. (C) Integrative analysis of Methylation patterns on CpG islands and RNA expression patterns could be explained with together. (D) The effect between chromatin modifications on genome and transcriptome patterns could be used to investigate gene regulation. (E) Chromatin structures involved in regulating gene expression levels.