Protocol for applying a network-enabled gene discovery pipeline to non-model plant species.

Dae Kwan Ko, Federica Brandizzi

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Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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5 · Who and what money

Authors and funding

2 authors.

Dae Kwan KoMSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA. Electronic address: dkko@msu.edu.

Federica BrandizziMSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA. Electronic address: fb@msu.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Identifying upstream regulators of key genes is essential for understanding gene regulatory mechanisms and translating these insights into functional targets. Here, we present a protocol for applying the network-enabled gene discovery pipeline (NEEDLE) to non-model plant species. We describe steps for environment setup, data preparation, computational analysis, expected outputs, and parameter considerations. NEEDLE integrates RNA sequencing (RNA-seq) processing, weighted gene co-expression analysis (WGCNA), Gene Network Inference with Ensemble of trees (GENIE3), and promoter conservation analysis to prioritize candidate transcriptional regulators. For complete details on the use and execution of this protocol, please refer to Ko and Brandizzi.

Indexed as

Plant sciencesRNAseqSystems biology

Identifiers

PMID42313566

DOI10.1016/j.xpro.2026.104641

PMCPMC13312126

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LicenceCC BY-NC-ND

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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.