Analysis of gene co-expression networks

Source code to systematically compare gene co-expression networks inferred from 15 healthy tissue and 15 cancer tissue bulk RNA-seq datasets to expert-curated gene regulatory, gene co-regulation and protein-protein interaction networks.

Installation of requirements

Install conda environment as follows (there also exists a requirements.txt)

conda env create -f environment.yml

Note: Additionally, modules itertools and Decimal were used, however no installation is required as they are provided with Python by default.

Reproducing the results

To reproduce the results:

Open a terminal and issue the following command:

python3 gist.py

This may take around 14 days.

Reproducing the plots from the manuscript

Reproducing Fig 2

Navigate to /plots/code/ and run figure_2.py. Plot saved as /plots/code/Figure 2.pdf.

Reproducing Fig 3

Navigate to /plots/code/ and run figure_3.py. Plot saved as /plots/code/Figure 3.pdf.

Reproducing Fig 4

Navigate to /plots/code/ and run figure_4.py. Plot saved as /plots/code/Figure 4.pdf.

Reproducing Fig 5

Navigate to /plots/code/ and run figure_5.py. Plot saved as /plots/code/Figure 5.pdf.

Reproducing Supplementary Fig 1

Navigate to /plots/code/ and run supplementary_figure_1.py. Plot saved as /plots/code/Supplementary figure 1.pdf.

Reproducing Supplementary Fig 2

Navigate to /plots/code/ and run supplementary_figure_2.py. Plot saved as /plots/code/Supplementary figure 2.pdf.

Reproducing Supplementary Fig 3

Navigate to /plots/code/ and run supplementary_figure_3.py. Plot saved as /plots/code/Supplementary figure 3.pdf.

Reproducing Supplementary Fig 4

Navigate to /plots/code/ and run supplementary_figure_4.py. Plot saved as /plots/code/Supplementary figure 4.pdf.

Reproducing Supplementary Fig 5

Navigate to /plots/code/ and run supplementary_figure_5.py. Plot saved as /plots/code/Supplementary figure 5.pdf.

Reproducing Supplementary Fig 6

Navigate to /plots/code/ and run supplementary_figure_6.py. Plot saved as /plots/code/Supplementary figure 6.pdf.

Reproducing Supplementary Fig 7

Navigate to /plots/code/ and run supplementary_figure_7.py. Plot saved as /plots/code/Supplementary figure 7.pdf.

Reproducing Supplementary Fig 8

Navigate to /plots/code/ and run supplementary_figure_8.py. Plot saved as /plots/code/Supplementary figure 8.pdf.

Reproducing Supplementary Fig 9

Navigate to /plots/code/ and run supplementary_figure_9.py. Plot saved as /plots/code/Supplementary figure 9.pdf.

Reproducing Supplementary Fig 10

Navigate to /plots/code/ and run supplementary_figure_10.py. Plot saved as /plots/code/Supplementary figure 10.pdf.

Reproducing Supplementary Fig 11

Navigate to /plots/code/ and run supplementary_figure_11.py. Plot saved as /plots/code/Supplementary figure 11.pdf.

Citing the work

Please cite the paper as follows:

• Will be updated once available.