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  1. IGB
  2. IGBF-4380

Gene Regulatory Networks

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          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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              bbendick Brandon Bendickson added a comment - - 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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              bbendick Brandon Bendickson added a comment - - 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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              bbendick Brandon Bendickson added a comment -

              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/

              Show
              bbendick Brandon Bendickson added a comment - 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/

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: