README.md

Controllability of the gene regulatory network in zebrafish embryogenesis

Park, J., Cho, K., Lee, J. et al. Controllability of the gene regulatory network in zebrafish embryogenesis. Sci Rep (2025). https://doi.org/10.1038/s41598-025-33869-9

1) What's in this repo

• data directory
  All inferred-GRN files are gene-gene edge list in NCOL-like format
  • interred_grn/: Reconstructed inferred-GRNs (per phase)
  • tf_list/: TF list
  • stage_segment_info/: Excel file containing developmental stage and segment information
  • result/: Various result files
• script directory
  workflow scripts (each script contains its own run commands and comments):
  • 01_manual_clustering/prepare_TENET_input.R: prepare inputs for TENET
  • 02_run_TENET/running_TENET.bash: run TENET
  • 03_run_netctrl/running_netctrl.bash: run netctrl
  • 04_find_critical_edge/: edge categorization and extract critical TF
• docs directory
  Reproducibility and provenance documents

2) Data sources & provenance

• Raw data
  Please download directly from the original paper (https://doi.org/10.1126/science.aar3131)
• TF list
  The TF list was obtained from AnimalTFDB 4.0 (https://doi.org/10.1093/nar/gkac907)

3) Third-party tools

• TENET
  The TENET is a Tool for Reconstructing Gene regulatory networks from scRNA-seq
  Paper: (https://doi.org/10.1093/nar/gkaa1014)

• netctrl
  The netctrl is a Tool for searching driver nodes in complex networks
  Paper: (https://doi.org/10.1038/nature10011)

Please see comments and commands inside each script under script/

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Licensing

• Code: Apache-2.0 (see LICENSE)
• Derived data (inferred-GRNs): CC BY 4.0 (see LICENSE-DATA)
• Raw data are NOT redistributed; please obtain from original sources.