[IGBF-4380] Gene Regulatory Networks - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
3
Epic Link:
Support NSF pollen grant
Sprint:
Fall 9, Spring 1

Description

GOAL:
To explore the current state of the union of gene regulatory networks.

Are there tools out there that we could apply to any of our current tomato data.
This could be a quick project in the works or a major component of the next tomato grant.

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Activity

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Robert Reid created issue - 16/Dec/25 9:29 AM

Robert Reid made changes - 16/Dec/25 9:29 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Robert Reid made changes - 16/Dec/25 9:29 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Brandon Bendickson added a comment - 16/Dec/25 11:01 AM - edited

Notes on Gene Regulation Tools
GENIE3:

"attempts to identify directed regulatory relationships—that is, which genes (particularly transcription factors) regulate which other genes."
"State of the art classic approach"
Supervised machine learning model
Uses gene expression data
Runs in R or Python
Generates a ranked list of likely regulatory links (Transcription Factor to Target Gene)
Requires a predefined list of transcription factors
1,970 citations.

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Brandon Bendickson added a comment - 16/Dec/25 11:01 AM - edited Notes on Gene Regulation Tools GENIE3: "attempts to identify directed regulatory relationships—that is, which genes (particularly transcription factors) regulate which other genes." "State of the art classic approach" Supervised machine learning model Uses gene expression data Runs in R or Python Generates a ranked list of likely regulatory links (Transcription Factor to Target Gene) Requires a predefined list of transcription factors 1,970 citations.

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Brandon Bendickson added a comment - 16/Dec/25 11:46 AM

Cool Tutorials

https://ngs101.com/how-to-build-gene-regulatory-networks-from-rna-seq-data-using-genie3-complete-step-by-step-guide-for-absolute-beginners/

https://ngs101.com/how-to-perform-master-regulator-analysis-on-rna-seq-data-using-regenrich-and-rtn-a-complete-beginners-guide/

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Brandon Bendickson added a comment - 16/Dec/25 11:46 AM Cool Tutorials https://ngs101.com/how-to-build-gene-regulatory-networks-from-rna-seq-data-using-genie3-complete-step-by-step-guide-for-absolute-beginners/ https://ngs101.com/how-to-perform-master-regulator-analysis-on-rna-seq-data-using-regenrich-and-rtn-a-complete-beginners-guide/

Ann Loraine made changes - 21/Dec/25 12:56 PM

Sprint

Fall 9 [ 232 ]

Fall 9, Spring 1 [ 232, 233 ]

Ann Loraine made changes - 21/Dec/25 12:56 PM

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