Contents

• Neko
  • version 0.9.0
• API
  • Network
    • neko.core.network.Network.load_network_from_sif
    • neko.core.network.Network.add_edge
    • neko.core.network.Network.remove_node
    • neko.core.network.Network.add_cascade_to_edge_list
    • neko.core.network.Network.add_node
    • neko.core.network.Network.add_paths_to_edge_list
    • neko.core.network.Network.complete_connection
    • neko.core.network.Network.connect_component
    • neko.core.network.Network.connect_genes_to_phenotype
    • neko.core.network.Network.connect_nodes
    • neko.core.network.Network.connect_subgroup
    • neko.core.network.Network.connect_to_upstream_nodes
    • neko.core.network.Network.convert_edgelist_into_genesymbol
    • neko.core.network.Network.filter_unsigned_paths
    • neko.core.network.Network.is_connected

Notebooks

Notebooks

• Usage
  • 1. Define the list of genes of interest
  • 2. Create a network using as input the gene set.
  • 3. Visualize final network
• Build network using user-defined resources
  • 1. Adding a resource already in Omnipath
  • 2. Adding a public database
  • 3. Build the network
• Build network based on kinase-phosphosite interactions
  • 1. Specify kinase-substrate interaction file and phosphosite effect annotation
  • 2. Add interactions as a resource database
  • 3. Define a set of phosphosites we are interested in
  • 4. Build network
• Connect to upstream components
  • 1. Import CollecTRI interactions from Omnipath
  • 2. Define the nodes of interest and create network object with CollecTRI interactions
  • 3. Connect nodes to upstream regulators
• Connect to downstream Gene Ontology terms.
  • 1. Build network
  • 2. Connect to Gene Ontology (GO) term
• Map tissue expression
  • 1. Import genes as network nodes
  • 2. Check if the genes are annotated in the tissue of interest (e.g., in colorectal cancer)
  • 3. Color nodes based on their presence/absence in the tissue of interest