getTagMatrix can accept type, by, upstream and downstream parameters to get tagmatrix according to different needs. getBioRegion can prepare the different regions for ChIP peaks to bind. Referring to the issue #16 and pull request#16, we developed and improved several functions support start site region, end site region and body region of Gene/Transcript/Exon/Intron/3UTR/5UTR. Profile of ChIP peaks binding to different regions 2015), ReactomePA (Yu and He 2016), clusterProfiler (Yu et al. Several visualization functions are implemented to visualize the coverage of the ChIP seq data, peak annotation, average profile and heatmap of peaks binding to TSS region.įunctional enrichment analysis of the peaks can be performed by my Bioconductor packages DOSE (Yu et al. Converting genome coordinations from one genome version to another is also supported, making this comparison available for different genome version and different species. Protein interaction hypothesis can be generated by mining data deposited in database. ChIPseeker (Yu, Wang, and He 2015) support statistical testing of significant overlap among ChIP seq data sets, and incorporate open access database GEO for users to compare their own dataset to those deposited in database. If two ChIP seq data, obtained by two different binding proteins, overlap significantly, these two proteins may form a complex or have interaction in regulation chromosome remodelling or gene expression. Even more important is applying to infer cooperative regulation. We can use it as an index to estimate how well biological replications are. ChIPseeker (Yu, Wang, and He 2015) was developed for annotating nearest genes and genomic features to peaks.ĬhIP peak data set comparison is also very important.

Annotation also create the possibility of integrating expression profile data to predict gene expression regulation.

After read mappings and peak callings, the peak should be annotated to answer the biological questions. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has become standard technologies for genome wide identification of DNA-binding protein target sites.

Mestrenova peak annotation