liver_1.3_network: Liver specific multi-layer network v1.3
In abodein/NetworkCosmeticEU: Liver network diffusion exploration
liver_1.3_network R Documentation
Liver specific multi-layer network v1.3
Description
The liver network is composed of 6 layers (gene, protein, drug/compound, pathway, side effect and Hepatox GO terms).
Usage
liver_1.3_network
Format
an igraph object
Details
First, the protein-protein interaction network layout wos build based on BioGRID (https://thebiogrid.org) and only proteins expressed in liver were kept (https://www.proteinatlas.org/humanproteome/tissue/liver).
Proteins were connected to an in-house gene coregulation network (ARACNE https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-S1-S7) with gene to protein coding information and Transctipted Factor (TF) to Targeted Genes (TG) with TF2DNA (https://www.fiserlab.org/tf2dna_db/), TRRUST https://www.grnpedia.org/trrust/ and Dorothea (https://saezlab.github.io/dorothea/). Only interactions between the present genes and proteins were included.
Drugs were extracted from DrugBank and were linked to their protein targets (https://drugbank.ca).
We used CHEMBL to add IC50 information when available for the HepG2 cell line and if the compound and its targets were present in the network.
Side Effects were extracted from SIDER and were linked to drugs (http://sideeffects.embl.de).
Proteins were also linked to Reactome pathways (https://reactome.org).
Finaly, GO terms linked to hepato-toxicicity were connected to gene and protein.
abodein/NetworkCosmeticEU documentation built on Jan. 29, 2024, 5:37 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| liver_1.3_network | R Documentation |
Liver specific multi-layer network v1.3
Description
The liver network is composed of 6 layers (gene, protein, drug/compound, pathway, side effect and Hepatox GO terms).
Usage
liver_1.3_network
Format
an igraph object
Details
First, the protein-protein interaction network layout wos build based on BioGRID (https://thebiogrid.org) and only proteins expressed in liver were kept (https://www.proteinatlas.org/humanproteome/tissue/liver).
Proteins were connected to an in-house gene coregulation network (ARACNE https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-S1-S7) with gene to protein coding information and Transctipted Factor (TF) to Targeted Genes (TG) with TF2DNA (https://www.fiserlab.org/tf2dna_db/), TRRUST https://www.grnpedia.org/trrust/ and Dorothea (https://saezlab.github.io/dorothea/). Only interactions between the present genes and proteins were included.
Drugs were extracted from DrugBank and were linked to their protein targets (https://drugbank.ca). We used CHEMBL to add IC50 information when available for the HepG2 cell line and if the compound and its targets were present in the network. Side Effects were extracted from SIDER and were linked to drugs (http://sideeffects.embl.de).
Proteins were also linked to Reactome pathways (https://reactome.org).
Finaly, GO terms linked to hepato-toxicicity were connected to gene and protein.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.