C. Elegans Network Connectivity and Correlated Gene Expression

This repository provides the code for reproducing a range of analyses involving processing connectivity and gene expression data for C. elegans, and running a range of analyses to relate patterns in both measurements.

Please read our paper, and if you use this code, please cite our paper:

A. Arnatkeviciute*, B.D. Fulcher*, R. Pocock, and A. Fornito. Hub connectivity, neuronal diversity, and gene expression in the C. elegans connectome, Plos Computational Biology, Published: February 12, 2018.

Contact Aurina Arnatkeviciute by email or twitter. Contact Ben Fulcher by email or twitter.

Dependencies: Brain Connectivity Toolbox, Version 2017-15-01.

Scripts

In order to reproduce data used in the analyses please download the contents of this repository.

Data files

Data files required for this project are hosted on this figshare repository. Please create a directory called Data in the root directory of this repository and download data there.

Data processing

After retrieving data, data files needed for analysis can be generated by running:

RegenerateData;

which is located in DataProcessing folder. It will create CElegansConnectivityData.mat file containing neuronal connectivity related data structure C and WS256_CertainEmptyEnrichedPartial.mat file containing gene expression related data structure G. Run LoadAllData to add all required paths and load necessary gene expression and connectivity data (stored in G and C data structures, respectively).

Gene expression matrix in the format 279 (neurons) x 948 (genes) is located in G.GeneExpData.Direct;

Binary connectivity matrices for 3 network representations (chemical synapses, electrical synapses, chemical and electrical synapses combined) are located in C.Adj_B cell.

Weighted connectivity matrices for 3 network representations (chemical synapses, electrical synapses, chemical and electrical synapses combined) are located in C.Adj_W cell.

Analysis

Figures in our paper can be regenerated using functions in the FigureGenerators directory. All scripts should be run from the root directory. Other relevant analysis scripts are in Analysis.