iTAR

'iTAR' is a bioinformatics software tool that has been specifically designed to identify target genes of transcription factors using ChIP-seq/ChIP-chip data. The software achieves this by implementing a Gaussian mixture model for p-value estimation, quantifying the strength of transcription factor binding-peak data, and performing GO enrichment analysis for the identified target genes.
The tool has been designed to address the limitations of the previously developed TIP (Target Identification from Profiles) probabilistic method for identifying TF target genes using ChIP-seq/ChIP-chip data. While TIP applies a conservative method to estimate the significance of target genes, it has been fine-tuned with key extensions to improve its sensitivity, accuracy, and usefulness.
TAR implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and accurately capturing the shape of TF binding profile distributions. It enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifying their strengths.
To facilitate the implementation and use of this software tool, it has been incorporated into a web server that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The iTAR web server also performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface, supports target gene identification in seven species ranging from yeast to human, and generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. It is useful in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights.