ArticleBioinformatics (Oxford, England)2015
Mango: a bias-correcting ChIA-PET analysis pipeline.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
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- Multidimensional mapping of stimulation-responsive regulatory elements and candidate causal variants in T cell activation.Science advances · 2026Article
- Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation.Nature cell biology · 2026Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- Splenic fibroblasts control marginal zone B cell movement and function via two distinct Notch2-dependent regulatory programs.Immunity · 2025Article
- Supervised Chromatin Loop Detection Using Peakachu Version 2.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Identifying genetic variants associated with chromatin looping and genome function.Nature communications · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
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- CD-Loop: a chromatin loop detection method based on the diffusion model.Frontiers in genetics · 2024Article
- Establishment of dsDNA-dsDNA interactions by the condensin complex.Molecular cell · 2023Article
- Regulation of CTCF loop formation during pancreatic cell differentiation.Nature communications · 2023Article
- Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network.Nature cardiovascular research · 2023Article
- Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation.Immunity · 2023Article
- DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks.PLoS computational biology · 2023Article
- Article
- Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation.Developmental cell · 2023Article
- CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.Nucleic acids research · 2023Article
- Nested epistasis enhancer networks for robust genome regulation.Science (New York, N.Y.) · 2022Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
motivationChromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.
resultsComparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs. AVAILABILITY AND IMPLEMENTATION: Mango is open source and distributed through github at https://github.com/dphansti/mango. CONTACT: mpsnyder@standford.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.