Study On NF-?B DNA-binding Profiles In Various Cells

The transcription factor(TF)binding profile is DNA sequences which could be recognized and bound by TF and relative affinities.At present,the construction of transcription factor binding profile in vivo is mainly based on chromosome immunoprecipitation(ChIP)followed high throughput sequencing(ChIP-Seq).ChIP-Seq combines ChIP with the next generation of sequencing technology.ChIP experiment is performed to capture the DNA fragments bound by transcription factors.Then these fragments are sequenced through the high-through put sequencing to get the binding information of the whole genome.With the rapid development of high-throughput sequencing technology,a large number of NF-?B binding profile data is abundant in the public database.Due to the large number of data analysis methods and software,there are few studies on normalizing high throughput data.In view of this situation,it is necessary to constructs a set of universal transcripts:(1)the original data collection and integration;(2)data format unified;(3)data quality control,evaluation;(4)reads mapping;(5)peak calling;(6)peak intersection overlap analysis,two peaks are determined to be overlapping in case they have a minimal overlapping interval of 1 bp;(7)motif discovery analysis.A total of 48 available NF-?B p65 ChIP-Seq data were collected from 14 articles,in which 12 articles were human ChIP-Seq data,2 articles were mouse ChIP-Seq Data.According to the data classfication of experiment groups and control groups,those data were calssfied into 27 groups.Therefore,all the NF-?B p65 ChIP-Seq data are compiled and the main processing results are uploaded to the server for inspection depend on ChIP-Seq data analysis process constructed above.The ChIP-Seq results of four cells lines with the same experimental conditions were used to analyse in this study.A total of 396 shared TF binding peaks were obtained,which were confirmed as highly conserved regions of NF-?B p65 interaction with DNA.A total of 342 genes were found to be closely related to inflammatory response and immune response,and they could regulate the metabolic process,cell growth,differentiation and apoptosis of cells,indicating that these related genes are closely related to NF-?B,and can play an important role in disease diagnosis.In summary,a standard unified NF-?B p65 ChIP-Seq data analysis process was constructed in this study,and a large number of ChIP-Seq data was analyzed according to this process to establish the p65 ChIP-Seq database.At the same time,the data of four kinds of cell lines were selected for further analysis,and 396 highly conserved binding peaks were obtained.GO analysis and signal pathway analysis were performed on the related genes of these binding regions.These NF-?B target genes are rather important resources for further disease diagnosis.