RegNetAgents: A Multi-Agent Framework for Cross-Network Regulatory Driver Identification in Cancer Genomics

-->

[Submitted on 16 Apr 2026]

Title:RegNetAgents: A Multi-Agent Framework for Cross-Network Regulatory Driver Identification in Cancer Genomics

View a PDF of the paper titled RegNetAgents: A Multi-Agent Framework for Cross-Network Regulatory Driver Identification in Cancer Genomics, by Jose A. Bird

View PDF HTML (experimental)

Abstract:We introduce RegNetAgents, an AI-oriented multi-agent framework for structured, query-driven regulatory candidate identification across heterogeneous gene regulatory networks. The system enables unified analysis of bulk tumor and single-cell-derived ARACNe networks by integrating TCGA-derived cancer networks with large-scale single-cell regulatory networks from the GREmLN project. For a given focal gene, the framework performs dual-network classification, cancer gene filtering using OncoKB annotations, and mode-of-action (MoA) assignment for tumor-derived regulatory relationships. Candidates are ranked by evidence consistency across networks (Both, TCGA-only, GREmLN-only). The system is implemented as a multi-agent LangGraph DAG workflow, accessible through a unified Python API and Model Context Protocol (MCP) client, operating as a downstream analytical layer over precomputed regulatory networks rather than a network inference method. Across eleven breast cancer (BRCA) and twelve colorectal cancer (COAD) focal genes, RegNetAgents identifies candidate regulators significantly enriched for OncoKB-annotated cancer genes. TCGA-derived candidates show strong enrichment (Stouffer Z = 6.69 for BRCA and 6.95 for COAD), while GREmLN-derived candidates also demonstrate significant enrichment (Z = 5.51 for BRCA and 7.06 for COAD; all p

new | recent | 2026-07

Change to browse by:

cs

References & Citations

NASA ADS

Google Scholar

Semantic Scholar

Loading...

Data provided by:

Bibliographic Tools

Bibliographic and Citation Tools

Bibliographic Explorer Toggle

Bibliographic Explorer (What is the Explorer?)

Connected Papers Toggle

Connected Papers (What is Connected Papers?)

Litmaps Toggle

Litmaps (What is Litmaps?)

scite.ai Toggle

scite Smart Citations (What are Smart Citations?)

Code, Data, Media

Code, Data and Media Associated with this Article

alphaXiv Toggle

alphaXiv (What is alphaXiv?)

Links to Code Toggle

CatalyzeX Code Finder for Papers (What is CatalyzeX?)

DagsHub Toggle

DagsHub (What is DagsHub?)

GotitPub Toggle

Gotit.pub (What is GotitPub?)

Huggingface Toggle

Hugging Face (What is Huggingface?)

ScienceCast Toggle

ScienceCast (What is ScienceCast?)

Demos

Demos

Replicate Toggle

Replicate (What is Replicate?)

Spaces Toggle

Hugging Face Spaces (What is Spaces?)

Spaces Toggle

TXYZ.AI (What is TXYZ.AI?)

Related Papers

Recommenders and Search Tools

Link to Influence Flower

Influence Flower (What are Influence Flowers?)

Core recommender toggle

CORE Recommender (What is CORE?)

Author

Venue

Institution

Topic

About arXivLabs

arXivLabs: experimental projects with community collaborators

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.

Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)