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On the correspondence between the transcriptomic response of a compound and its effects on its targets

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General Info

This repository contains code and data for our paper, "On the correspondence between the transcriptomic response of a compound and its effects on its targets" (Hart et al., 2023), which investigates the agreement between transcriptomic profiles and target information for over 2,000 chemical compounds.

Citation

If you have found our manuscript useful in your work, please consider citing:

Hart C. E, Ence D., Healey, D., Domingo-Fernández, D. (2023). On the correspondence between the transcriptomic response of a compound and its effects on its targets. BMC Bioinformatics. 24, 207. DOI

Dataset

The data comes from ChemPert a tools containing mappings between chemical perturbation and transcriptional response for non-cancer cells.

The ChemPert dataset and other used and generated data is available at Zenodo DOI.

Code

The project has the following structure:

|-- data (main data folder)
|   |-- ChemPert_data
|   |-- Protein_classes
|   |-- Protein_mappings
|   |-- Protein_pathways
|   |-- Transcriptional_data_frames
|   |-- target_data_frames
|-- figures (paper figures)
`-- notebooks (correlation analyses)
    |-- 1_chempert_preprocessing.ipynb
    |-- 2_correlation_chempert.ipynb
    |-- 2.1_DEG_analysis.ipynb
    |-- 3_pathway_info_for_target_vectors.ipynb
    |-- 3.1_random_pathway_target_vectors.ipynb
    |-- 3.2_random_network_target_vectors.ipynb
    |-- 4_pathway_correlation_analysis.ipynb
    |-- 4.1_random_networks_analysis.ipynb
    |-- 4.2_random_pathways_analysis.ipynb
    |-- 4.3_multifactorial_analysis.ipynb
    |-- 5_similar_transcriptomic_profiles.ipynb
    |-- 6_Network_figure.ipynb
    |-- utils.py
    `-- viz.py