Developing A Web Server For Functional Annotation Of Transcription Factor ChIP-seq And Its Application

ChIP-seq is a broadly used technique for studying the transcriptional regulatory functions of transcription factors(TFs).However,the webservers available for functional enrichment analysis based on ChIP-seq peaks are still limited.In the first part of this study,we developed Cistrome-GO,a website that conducts functional enrichment analyses of gene regulation by TFs.Cistrome-GO has two working modes:solo mode and ensemble mode.In solo mode,the regulatory potential score of a gene is calculated as the sum of weighted regulatory potential of each peak,and for each peak,the weight of regulatory potential is delayed exponentially upon its distance to the gene’s transcription start site.In ensemble mode,differential expression information upon the perturbation of a TF(such as overexpression,knock-down or knock-out)are incorporated,and two ranks(based on regulatory potential score and differential expression)are integrated by rank product.In both modes of Cistrome-GO,the top ranked genes are most likely to be directly regulated by the TF.Cistrome-GO performs GO and pathway enrichment analysis based on gene ranks using the minimum hypergeometric test,instead of selecting targets using an arbitrary cutoff.Cistrome-GO has three unique features compared to published webservers.First,Cistrome-GO uses continuous values instead of binary values to measure each gene’s potential to be regulated by a TF.Second,Cistrome-GO performs GO term enrichment analysis based on gene rank.Third,Cistrome-GO can integrate differential expression information.Cistrome-GO is a powerful and user-friendly website for functional enrichment annotation of TF regulation.Users can upload a ChIP-seq peak file for a TF in human or mouse,together with an optional differential expression file.With a table of gene regulatory potential ranks and tables of GO and pathway enrichment as output,the Cistrome-GO webserver gives biologists a deeper understanding of TFs’ regulatory functions.It is important to study the uniformity and diversity of TFs’ functions under different cell statuses.However,such a consideration is not involved in available classification approaches of TFs.In the second part of this study,based on Cistrome-GO,we performed ChIP-seq functional annotation atlas analysis for TFs in human.We applied Cistrome-GO to each published ChIP-seq data for TFs in human,and generated a matrix of GO enrichment scores for ChIP-seq peaks.Similar to single-cell transcriptome analysis strategy,we conducted ChIP-seq functional annotation atlas analysis for TFs in human.First,we presented a TFs classification strategy based on ChIP-seq functional annotation atlas,and identified 32 functional annotation classes.We further conducted TFs co-enrichment networks,reflecting the uniformity of different TFs in terms of functional annotation.Second,we introduced cluster aggregation index for quantitatively measuring the diversity of functional annotations of a TF among different cell statuses.Focusing on the uniformity and diversity of TFs’ functions under different cell statuses,this study presented analysis approached of ChIP-seq functional annotation atlas,and provided a novel TFs classification strategy.In summary,this study presented Cistrome-GO,a powerful functional enrichment annotation webserver for TF regulation,and performed conducted ChIP-seq functional annotation atlas analysis for TFs in human based on Cistrome-GO.This study can help biologists deeply understand TFs’ regulatory functions,together with the uniformity and diversity of TFs’ functions under different cell statuses.