Welcome to CoRe’s documentation!
Communication through Reactome and Interactome (CoRe) is an open-source scientific software to model human biological pathways as information transferring networks. CoRe uses the Reactome and the Human Reference Interactome databases to construct communication network models for human biology.
CoRe also uses the gene sets from the c5 collection in the MSigDB database to identify the significant biological processes using Gene Ontology over-representation analysis.
This version of CoRe computes the information transfer in the immune system due to interactions with SARS-CoV-2 proteins.
- Author:
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- References:
If you are using any part of CoRe, please cite: S. Sarkar, Communication network model of the immune system identifies the impact of interactions with SARS-CoV-2 proteins, arXiv (2022)
Other references on the use of information theory for biochemical networks. Sarkar S, Hubbard JB, Halter M, Plant AL. Information thermodynamics and reducibility of large gene networks. Entropy. 2021 Jan 1;23(1):63
Contents:
- Network construction
- Adding human PPI to the network
- Specifying information sources
- Computing information transfer
- Communicated proteins
- Communicated genes overrepresentation analysis
- Drug efficacy
- Computing efficacy (protein expression)
- ncip
ncipncip.add_edges()ncip.apply_BC()ncip.construct_C()ncip.construct_edges()ncip.construct_exo_edges()ncip.disconnect_drug_nodes()ncip.disconnect_nodes()ncip.entropy_drop_and_gain()ncip.get_final_state()ncip.get_final_state_old()ncip.initialize_network_state()ncip.load_data()ncip.load_graph()ncip.make_graph()ncip.save_edges_and_nodes()ncip.save_network()ncip.save_nullspace()ncip.state_entropy()ncip.write_nodes_and_edges()
- fnGO
- Dependencies