ArticleGenome biology2014
OncoCis: annotation of cis-regulatory mutations in cancer.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases.Frontiers in bioscience (Scholar edition) · 2024Review
- CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines.Database : the journal of biological databases and curation · 2023Article
- Article
- Regulatory variants: from detection to predicting impact.Briefings in bioinformatics · 2019Review
- atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding.Bioinformatics (Oxford, England) · 2019Article
- In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma.International journal of molecular sciences · 2019Article
- Finding cancer driver mutations in the era of big data research.Biophysical reviews · 2019Review
- Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks.Genome medicine · 2017Article
- Functional variomics and network perturbation: connecting genotype to phenotype in cancer.Nature reviews. Genetics · 2017Review
- Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2017Article
- SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity.Nucleic acids research · 2017Article
- Exome-based Variant Detection in Core Promoters.Scientific reports · 2016Article
- A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers.Nature communications · 2016Article
- Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer.PLoS genetics · 2016Review
- Role of non-coding sequence variants in cancer.Nature reviews. Genetics · 2016Review
- Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.PLoS computational biology · 2015Article
- The search for cis-regulatory driver mutations in cancer genomes.Oncotarget · 2015Review
- Reclassification of Splicing Gene Variants in Hereditary Cancer: Cases Report and Literature Review.In vivo (Athens, Greece)Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing has enabled the identification of thousands of somatic mutations within non-coding genomic regions of individual cancer samples. However, identification of mutations that potentially alter gene regulation remains a major challenge. Here we present OncoCis, a new method that enables identification of potential cis-regulatory mutations using cell type-specific genome and epigenome-wide datasets along with matching gene expression data. We demonstrate that the use of cell type-specific information and gene expression can significantly reduce the number of candidate cis-regulatory mutations compared with existing tools designed for the annotation of cis-regulatory SNPs. The OncoCis webserver is freely accessible at https://powcs.med.unsw.edu.au/OncoCis/.
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Registered trials
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.