Zebrafish

Orthologous Protein Identification

• Run OrthoFinder to find orthologs between zebrafish and humans.
• Separate identified proteins by chromosome and conservation index.

Protein Characterization

Calculate alignment variables for each ortholog:

• % amino acid identity
• % similar/positive amino acids
• % coverage
• E-value

Functional Profile Analysis

Use GO to analyze biological process, molecular function, and cellular component.

• Use KEGG to identify pathways.
• Use SignalP to identify signal peptides.

Target Selection in Epilepsy

Identify canonical orthologous proteins involved in epileptic seizures in zebrafish.

• Level of conservation
• Function (biological, molecular, cellular)
• Involved pathways
• Signal peptides
• Type of orthology (one-to-one, one-to-two, one-to-more)

Paralogous Analysis

• Calculate alignment variables for duplicates.

Structure

/zebrafish
│
├── /data
│   ├── /raw
│   │   └── orthofinder_output.zip
│   ├── /processed
│   │   ├── orthologous_proteins.csv
│   │   ├── paralogoues_proteins.csv
│   │   └── other_analyses
│   └── /results
│       ├── GO_analyses
│       ├── KEGG_analyses
│       └── SignalP_analyses
│
├── /scripts
│   ├── /orthofinder
│   │   └── orthofinder_script.sh
│   ├── /functional_analysis
│   │   ├── GO_script.sh
│   │   ├── KEGG_script.sh
│   │   └── SignalP_script.sh
│   └── /paralogoues_analysis
│       
│
├── /documentation
│   ├── README.md
│   ├── CONTRIBUTING.md
│   ├── LICENSE.md
│   └── /reports
│
│
├── /figures
|
│
├── .gitignore
│
└── README.md