iTAD integrates two commonly used downstream analysis tool to interpret the regulatory function of loops furtherly. The input of loop file could be predicted result generated by EPI Prediction Module, as well as the uploaded 3D contact data generated by Hi-C, ChIA-PET, HiChIP and so on [check guidance of format].
Motif analysis is cooperated with RNA-seq expression data to show the significant enrichment. Users can select the interested motif to show the visualization of motif ranking. Motif analysis is implemented by Homer (1) and the cooperation analysis is taken by homemade script. The motif ranking plot is drawn by Echarts[API].
GO analysis is taken on the nearest genes of loop anchors, three types of terms are provided: sub-Ontology (including Biological Process, Cellular Component, Molecular Function), KEGG pathway, and REACTOME Gene Sets. Which is implemented by clusterProfiler (2). The GO terms ranking plot is drawn by Echarts[API].
1. Heinz S, Benner C, Spann N, Bertolino E et al., 2010. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 28;38(4):576-589.
2. Yu G, Wang LG, Han Y, He QY., 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology. 16:284-7.