ArticleNucleic acids research2015
Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Conservation and divergence of canonical and non-canonical imprinting in murids.Genome biology · 2023Pooled it
- The superpowers of imprinting control regions.Genome research · 2026Review
- Long-read sequencing disentangles isoform complexity at allele-specific loci.Scientific reports · 2025Article
- ASET: an end-to-end pipeline for quantification and visualization of allele specific expression.BMC bioinformatics · 2025Article
- Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome.Nucleic acids research · 2025Article
- Cell-cell communication-mediated cell-type-specific parent-of-origin effects in mammals.Nature communications · 2025Article
- Aging promotes reactivation of the Barr body at distal chromosome regions.Nature aging · 2025Article
- X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes.Nature communications · 2024Article
- Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Haplotype-resolved 3D chromatin architecture of the hybrid pig.Genome research · 2024Article
- Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation.Human molecular genetics · 2023Article
- Allele-specific regulatory effects on the pig transcriptome.GigaScience · 2022Article
- From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo.Nature reviews. Genetics · 2022Review
- Presence of H3K4me3 on Paternally Expressed Genes of the Paternal Genome From Sperm to Implantation.Frontiers in cell and developmental biology · 2022Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages.Developmental cell · 2021Article
- Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3.Nature communications · 2021Article
- Modern epigenetics methods in biological research.Methods (San Diego, Calif.) · 2021Review
- Article
- ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses.Bioinformatics (Oxford, England) · 2020Article
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Authors and funding
8 authors.
Funding
Abstract
Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the 'allelome' by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.
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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.