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Updated: Apr 27, 2026

A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

Published on: July 18, 2025

Integrating diverse datasets improves developmental enhancer prediction.

Genevieve D Erwin¹, Nir Oksenberg², Rebecca M Truty³

¹Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.

Plos Computational Biology

|June 27, 2014

Summary

This summary is machine-generated.

EnhancerFinder integrates multiple data types to identify developmental enhancers and predict tissue specificity. This new method improves enhancer identification and provides genome-wide predictions for non-coding DNA research.

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A Rapid In Vivo Bioassay for Developmentally Active Enhancers

A Rapid In Vivo Bioassay for Developmentally Active Enhancers

Area of Science:

Genomics
Developmental Biology
Bioinformatics

Background:

Gene-regulatory enhancers control gene expression and development.
Existing methods for enhancer identification use limited data types.

Purpose of the Study:

To develop and validate EnhancerFinder, an integrative method for identifying developmental enhancers and predicting their tissue specificity.
To provide genome-wide predictions of developmental enhancers.

Main Methods:

EnhancerFinder uses a two-step approach integrating DNA sequence motifs, evolutionary patterns, and functional genomics data via multiple kernel learning.
Trained on experimentally verified human developmental enhancers from the VISTA Enhancer Browser.
Evaluated using cross-validation and compared to single-data type approaches.

Main Results:

EnhancerFinder significantly improves enhancer identification compared to single-data type methods.
Identified 84,301 developmental enhancers and their tissue specificities across the human genome.
Predictions are enriched near genes involved in tissue-specific functions and GWAS lead SNPs.
In vivo validation confirmed novel embryonic gene regulatory enhancers.

Conclusions:

EnhancerFinder is an effective integrative tool for identifying and characterizing developmental enhancers.
Genome-wide predictions offer valuable functional annotations for human non-coding DNA.
The freely available UCSC Genome Browser track facilitates further research in developmental biology.