Skip to main content
Fig. 1 | BMC Genomics

Fig. 1

From: iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data

Fig. 1

An overview of the iTAR web server. a The portal page of the iTAR web server: wig, bigwig, and bedgraph files in rar or gz format can be used for upload. b The waiting page: after a wiggle file is uploaded, a waiting page will be shown to the user, updating job status every 5 s. For this example, we used the ENCODE STAT3 ChIP-seq data in HeLa-S3 cells. c The characteristic binding profile of an example TF. It shows the aggregation plot of TF binding in a 20 kb DNA region centered at the transcriptional start site (TSS). This plot can be used to make a rough evaluation of the data quality. In general, we expect to see a peak near by the TSS. d The density plot of normalized regulatory scores (Z score). For each gene, the iTAR server will calculate a regulatory score, measuring the binding strength of a TF to the gene. The regulatory scores for all genes will then be normalized, and p-values will be calculated based on a single normal distribution model or a mixture normal distribution model. e A list of significant target genes and the associated TF binding site: significant RefSeq genes, gene symbols and P-values will be shown. P-value 1 is estimated based on the mixture normal distribution model, and P-value 2 is estimated based on the single normal distribution model. The summit location is the summit of the binding peak from TSS. f GO enrichment analysis with the target genes

Back to article page