The cistrome refers to "the set of cis-acting targets of a trans-acting factor on a genome-wide scale, also known as the in vivo genome-wide location of transcription factor binding-sites or histone modifications". Here we build integrative analysis pipelines (Cistrome) to help experimental biologists, and conduct efficient data integration to better mine the hidden biological insights from publicly available high throughput data.
An integrative and reproducible bioinformatics data analysis platform based on Galaxy open source framework. Besides standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery.
A new portal to browser public ChIP-seq and DNase-seq datasets. Besides providing a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human, it also provides functions to analysis and visualize these datasets.
A comprehensive resource for predicted transcription factor (TF) targets and enhancer profiles in cancers. The prediction was from integrative analysis of TCGA expression profiles and public ChIP-seq profiles.