This repository contains the scripts used for the project titled: "Gene network module changes associated with the vertebrate fin to limb transition"
The scripts are arranged into following folders
Gene_extractor: A script to extract genes annotated directly to a given anatomical entity. Used to prepare the genes with original annotations.
Anatomy_part_extractor: A script to extract genes annotated to the parts of a given anatomical entity. Used to prepare the genes with original annotations.
Precision_threshold_variation: Using the trial and error method to select a precision threshold for module extraction.
Threshold_mdetection: Selects candidate genes for a given anatomical entity and extracts the module based on a given precision threshold score.
Module_net_prediction: Predict scores for each unknown gene based on Hishigaki network-based candidate gene prediction method. Moreover, contains a script for evaluating the network-based candidate gene prediction performance using leave-one-out cross-validation to generate ROC and precision-recall curves
Module_comparison: Compares two given modules (e.g., pelvic fin vs hindlimb). Also, contains a script to distinguish whether the compared genes are directly annotated or annotated to parts or precursors.
Weighted_degree_comparison: Performs comparisons of weighted degrees for predicted vs genes with original annotations and module-specific vs conserved genes
Uberon_enrichment_analysis: Perform enrichment analysis using Uberon terms and Fisher's exact test for a given gene list