mappings 0.0.1

Mapping and Analysis of Phosphorylation Pathways Identified through Network/Graph Signalling

# 🗺 MAPPINGS v0.0.1

## Mapping and Analysis of Phosphorylation Pathways Identified through Network/Graph Signalling

Mappings is a tool for blah blah.

It analyses kinexus chip data to find..

Maybe put a picture here or something. The sky is the limit.

First described by our names here: (Not the real article, but just showing you can put links)

[Network analysis of large phospho-signalling datasets: application to Plasmodium-erythrocyte interactions](https://www.biorxiv.org/content/10.1101/2021.05.07.443051v1)

and it looked pretty good doing it!


Designed and programmed with love by Dr. Jack Adderley and Finn O’Donoghue.

## Installation

pip install mappings

## Usage

mappings [OPTIONS] ARRAY_DATA_PATH OUTPUT_PATH

or

python -m mappings [OPTIONS] ARRAY_DATA_PATH OUTPUT_PATH

### Options

--nwalks INTEGER

Number of walks.

--connection_network_path PATH

Network of known phosphorylation connections.

## Input / Output Specification

### Array Data Sort of comes from kinexus.

CSV file with headers:

• Uniprot ID

• Protein

• Phospho Site (Human),

• UMean

• UMean Error (%)

• TMean

• TMean Error (%)

### Output Data For use in Cytoscape or some other analysis program.

CSV file with headers:

• Kinase

• Substrate

• cdf_x

• INVLog2FoldChange

• …etc

### Connection Network Accumulated from literature reports. Updated version may be available under data/input/NetworkComplete.csv Please email the authors, or submit a pull request to update this file with any new data.

CSV file with headers: - Phosphosite - Kinase_uniprot_ID - Substrate_uniprot_ID - SubID_phosphosite - Substrate_effect - Kinase - Substrate

## Publications

• …et al. 2021

• [Review by highly respected bioinformatics group et al., 2022](https://www.google.com/search?q=most+important+bioinformatics+tools+of+all+time)