Getting Started

Here we guide you to get started on using FISHNET for your next project.

Note: if you use FISHNET in published research, please cite the following paper:

Acharya et al., FISHNET: A Network-based Tool for Analyzing Gene-level P-values to Identify Significant Genes Missed by Standard Methods, doi:10.1101/2025.01.29.635546.

Table of contents

1. Installation
2. Quick start
   1. Execution
   2. Output files

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Installation

Clone the FISHENT GitHub repository and cd into the local repository:

$ git clone https://github.com/BrentLab/fishnet.git
$ cd fishnet/

Run FISHNET on test data to verify successful installation:

$ ./fishnet.sh --test

Note: If your platform does not support Docker (e.g. in a HPC environment), use the --singularity flag:

$ ./fishnet.sh --test --singularity

Quick start

Execution

Here we show the most basic steps for a FISHNET analysis. There are a variety of configuration options which are detailed in Configuration. This code chunk assumes that you have an input summary statistics file at /path/to/input/file.csv (comma-separated with columns named “Genes” and “p_vals”) and a set of tab-delimited .txt network module files at /path/to/modules/directory/.

$ ./fishnet.sh \
    --trait /path/to/input/file.csv \
    --modules /path/to/modules/directory/

This will run both stages of FISHNET with 10 permutations (by default) using the default thresholding method (by default).

Output files

The output files are saved in a results/ subdirectory (by default) relative to the current working directory where you launch fishnet.sh. Here, we guide you through the expected output directory structure.

1. The results/data/ directory stores the input summary statistics file and the input module networks. In addition, the results/data/<trait>RR/ directory saves the uniformly distributed p-values based on the input summary statitics file as <trait>RR.csv.

   results/
   └── data/
    └── <trait>/
        └── 0-<trait>.csv
    └── <trait>RR/
        └── <trait>RR.csv
    └── modules/
        └── <module_algorithm>/
            ├── <module1>.txt
            ├── ...
            └── <module3>.txt
   

2. The results/<trait>/ directory stores results for the input summary statistics p-values. The enriched_modules/ directory lists significantly enriched modules for each network. The GO_summaries/ directory lists statistics for the GO overrepresentation analysis. The FISHNET genes for the trait and the network the genes originate from can be found in summary/<network>_<trait>_fishnet_genes_<FDR-threshold>.csv

results/
└── <trait>/
    └── background_genes/
        ├── <module_algorithm>-<module1>.txt
        ├── ...
        └── <module_algorithm>-<module3>.txt
    └── enriched_modules/
        ├── <trait>-<module3>
        └── └── sig_<trait>-<module3>-179.txt
    └── GO_summaries/
        └── <trait>/
            ├── GO_summaries_0-<trait>_<module1>/
            ├── GO_summaries_0-<trait>_<module3>/
            └── └── sig_<trait>_0-<trait>_<module3>_179.csv
    ├── <trait>.txt
    └── masterSummaries/
        └── summaries/
            ├── <trait>_0-<trait>_<module1>.csv
            ├── ...
            └── <trait>_0-<trait>_<module3>.csv
    ├── master_summary.csv
    ├── master_summary_filtered.csv
    ├── master_summary_filtered_parsed.csv
    └── results/
        └── raw/
            ├── <module1>_0-<trait>_<module1>_or_fishnet_genes.csv
            ├── <module1>_0-<trait>_<module1>_or_summary.csv
            ├── ...
            ├── <module3>_0-<trait>_<module3>_or_fishnet_genes.csv
            └── <module3>_0-<trait>_<module3>_or_summary.csv
    └── summary/
        ├── 0-<trait>_<network1>_summary.csv
        ├── <network1>_<trait>_fishnet_genes_<FDR-threshold>.csv 
        ├── 
        ├── 
        ├── 0-<trait>_<network2>_summary.csv
        └── <network2>_<trait>_fishnet_genes_<FDR-threshold>.csv 

1. The results/<trait>RR/ directory stores results for the permutations. Subdirectory contents are identical to the original <trait> directory as described above.

   results/
   └── <trait>RR/
    ├── background_genes/
    └── enriched_modules/
        ├── <trait>RR-<module1>/
        ├── <trait>RR-<module3>/
        ├── GO_summaries/
        └── <trait>RR/
    ├── <trait>RR.txt
    └── masterSummaries/
        └── summaries/
    ├── master_summary.csv
    ├── master_summary_filtered.csv
    └── master_summary_filtered_parsed.csv