Arabidopsis kinase genetic interaction prediction project

Raw data:

• All the raw datasets used for this project are in the folder /home/seguraab/ara-kinase-prediction/data/

• Paper: https://doi.org/10.1093/molbev/msab111 (Cusack et al., 2021 MBE)

• Data retrieval sources:

  • GitHub: https://github.com/ShiuLab/Manuscript_Code/tree/master/2021_Arabidopsis_redundancy_modeling

  • Zenodo: https://zenodo.org/records/3987384

    • Dataset_2.txt: training set feature matrix (inclusive genetic redundancy gene pairs [RD9]) in /home/seguraab/ara-kinase-prediction/data/2021_cusack_data/
    • Dataset_4.txt: training set feature matrix (extreme genetic redundancy gene pairs [RD4]) and testing set (kinases) in /home/seguraab/ara-kinase-prediction/data/2021_cusack__data/

  • From the MSU hpcc: /mnt/research/ShiuLab/21_arabidopsis_redundancy

    • This folder contains the raw and pre-processed features from Cusack et al., 2021
    • Saved to /home/seguraab/ara-kinase-prediction/data/2021_cusack_data/21_arabidopsis_redundancy

• Feature name list:

  • Supplemental_tables_revision.xlsx: Supplemental table 1 (4,116 features) in /home/seguraab/ara-kinase-prediction/data/2021_cusack_data/

• Instances:

  • Training data:
    • interactions_fitness.txt: Melissa's duplicate gene pair instances with binary genetic interaction label (0 for not interacting, 1 for interacting)
  • Test data:
    • FILE TBD: n number of kinase genes from Dataset_4.txt that are not overlapping with interactions_fitness.txt