ArticleNucleic acids research2016
EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development.bioRxiv : the preprint server for biology · 2025Article
- Major cell-types in multiomic single-nucleus datasets impact statistical modeling of links between regulatory sequences and target genes.Scientific reports · 2023Article
- Article
- Patient-Specific TBX5-G125R Variant Induces Profound Transcriptional Deregulation and Atrial Dysfunction.Circulation · 2022Article
- Common Genetic Variants Contribute to Risk of Transposition of the Great Arteries.Circulation research · 2022Article
- ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.PLoS computational biology · 2021Article
- Genome-Wide Analysis Identifies an Essential Human TBX3 Pacemaker Enhancer.Circulation research · 2020Article
- Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis.Circulation research · 2020Article
- T-box transcription factor 3 governs a transcriptional program for the function of the mouse atrioventricular conduction system.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Genetic and Epigenetic Control of Heart Development.Cold Spring Harbor perspectives in biology · 2020Review
- Epigenetic and Transcriptional Networks Underlying Atrial Fibrillation.Circulation research · 2020Review
- From Genome-Wide Association Studies to Cardiac Electrophysiology: Through the Maze of Biological Complexity.Frontiers in physiology · 2020Review
- An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo.Nature communications · 2019Article
- Identification of atrial fibrillation associated genes and functional non-coding variants.Nature communications · 2019Article
- Identifying pathogenic variants in the Follistatin-like 1 gene (FSTL1) in patients with skeletal and atrioventricular valve disorders.Molecular genetics & genomic medicine · 2019Article
- A neural network based model effectively predicts enhancers from clinical ATAC-seq samples.Scientific reports · 2018Article
- Sequence based prediction of enhancer regions from DNA random walk.Scientific reports · 2018Article
- Structure and function of the Nppa-Nppb cluster locus during heart development and disease.Cellular and molecular life sciences : CMLS · 2018Review
- Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regulatory DNA elements, short genomic segments that regulate gene expression, have been implicated in developmental disorders and human disease. Despite this clinical urgency, only a small fraction of the regulatory DNA repertoire has been confirmed through reporter gene assays. The overall success rate of functional validation of candidate regulatory elements is low. Moreover, the number and diversity of datasets from which putative regulatory elements can be identified is large and rapidly increasing. We generated a flexible and user-friendly tool to integrate the information from different types of genomic datasets, e.g. ATAC-seq, ChIP-seq, conservation, aiming to increase the ease and success rate of functional prediction. To this end, we developed the EMERGE program that merges all datasets that the user considers informative and uses a logistic regression framework, based on validated functional elements, to set optimal weights to these datasets. ROC curve analysis shows that a combination of datasets leads to improved prediction of tissue-specific enhancers in human, mouse and Drosophila genomes. Functional assays based on this prediction can be expected to have substantially higher success rates. The resulting integrated signal for prediction of functional elements can be plotted in a build-in genome browser or exported for further analysis.
Indexed as
Identifiers
What OpenQuestion holds
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.