FactorDNA

FactorDNA is a framework and data standard designed to annotate DNA sequences with functional factors that influence gene regulation. It integrates data on transcription factors, epigenetic marks, chromatin accessibility, and motifs to enable systematic regulatory analysis.

The FactorDNA data model captures factor identity, binding motifs, and quantitative measures such as affinity or occupancy, plus contextual metadata (cell type, developmental stage) and experimental evidence (source, method, confidence). It references external resources for traceability.

It originated from collaborative efforts among computational biology and molecular biology groups aiming to standardize regulatory annotations across datasets. The project emphasizes open standards and interoperability and has been used in pilot studies for human and model organisms.

Technically, FactorDNA can be serialized in JSON or RDF and interoperates with genome browsers and variant interpretation pipelines. It supports querying factor-gene associations and can be extended with user-defined factors. Tools can map sequence variants to regulatory impact using FactorDNA annotations.

Applications include annotation of regulatory elements, interpretation of non-coding variants in clinical genomics, and design of synthetic regulatory circuits. It enables meta-analyses of factor usage across tissues and conditions.

The project is maintained by a community governance model with regular updates. Ongoing work aims to expand coverage, enhance evidence tracking, and align with data sharing and licensing norms.