Browse Code
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers. The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn), an integrated database for annotating regulatory noncoding somatic mutations in human cancers by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms.
Features
- Collects all of the somatic mutations identified by TCGA and ICGC, and somatic mutations deposited in COSMIC and ClinVar;
- Constructs more than 10 million enhancer target interactions by multiple predictions from multiple resources;
- Incorporates 127 tissue/cell type-specific epigenomic data from ENCODE and Roadmap epigenomics project;
- Integrates motifs of 2817 transcriptional regulators from 4 public resources and predicts the effects of mutations on the binding motifs;
- Uniformly processes of 3C/4C/5C/Hi-C/ChIA-PET data and generates significant interactions at high resolution across 80 tissues/cell types;
- Provides comprehensive functional annotation and prediction of the regulatory somatic mutations;
- Equips a highly interactive visualization function for mutation-target interaction;
- Includes multiple concept of QTLs, including eQTLs, hQTLs, mQTLs and dsQTLs;
- Provides the prioritization of gene targets of regulatory mutations by network diffusion;
- Establishes weighted gene co-expression networks for 36 tumor types from TCGA projects.
Project Samples
