ArticleNucleic acids research2019
OncoBase: a platform for decoding regulatory somatic mutations in human cancers.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 48 citations in OpenAlex.
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- Non-Coding RNAs Extended Omnigenic Module of Cancers.Entropy (Basel, Switzerland) · 2024Article
- Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements.Cellular and molecular life sciences : CMLS · 2024Review
- Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues.Briefings in bioinformatics · 2024Article
- KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species.Nucleic acids research · 2024Article
- LncSEA 2.0: an updated platform for long non-coding RNA related sets and enrichment analysis.Nucleic acids research · 2024Article
- eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse.Nucleic acids research · 2024Article
- Article
- CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines.Database : the journal of biological databases and curation · 2023Article
- SEdb 2.0: a comprehensive super-enhancer database of human and mouse.Nucleic acids research · 2023Article
- ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms.Nucleic acids research · 2023Article
- CRdb: a comprehensive resource for deciphering chromatin regulators in human.Nucleic acids research · 2023Article
- Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase.Nucleic acids research · 2023Article
- CanMethdb: a database for genome-wide DNA methylation annotation in cancers.Bioinformatics (Oxford, England) · 2023Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
Corrections and comments
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Authors and funding
13 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput sequencing 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 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects 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. It employs informative visualization tools to display the integrated local and 3D chromatin signatures and effects of somatic mutations on regulatory elements. Enhancer-promoter interactions estimated from chromatin interactions are integrated into a network diffusion system that quantitatively prioritizes somatic mutations and target genes from a large pool. Thus, OncoBase is a useful resource for the functional annotation of regulatory noncoding regions and systematically benchmarking the regulatory effects of embedded noncoding somatic mutations in human carcinogenesis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.