BiologicalNetworks

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Merging network, pathways
  • Wang January 20
    Hi there,

    I am new to BiologicalNetworks and am currently using it to view gene interaction networks and pathways. I am wondering how i could build interaction networks for say NF-kB and EGFR at the same time and then how i could merge these two networks?

    Also, is there a way to display these interactions with other proteins in a certain
    pathway for example from KEGG or Reactome?

    Thanks!

  • BN_ January 20
    Hi,

    you can start constructing netwrok for NF-kB and EGFR at the same time.
    First, search "NF-kB, EGFR" in the main Search Bar (top right); then selecting
    from the Search Results panel NF-kB and EGFR from respective organism by righ mouse click start "Build Pathway Wizard".

    In the Build Pathway Wizard you can construct interaction networks of different types (direct/indirect interactions, 2-level neighbors, shortest paths, etc) for these and other genes/proteins. It has various filtering options on the types of objects/relations.

    In the same Build Pathway Wizard there is a method "Intersection with Canonical Pathways", that finds intersection of your interaction network with Canonical Pathways.
    It has an option to set a Source Database for pathways, e.g. KEGG, NCI-Nature, Reactome,
    HumanCyc, etc.

    Hope this helps.
    Please, let me know if you have more questions.

  • Wang January 26
    Hi,

    Thanks for your help.

    I could do the Canonical Pathways search and do microarray overlay on these pathways.
    I have a question: what are the Imaging Pathways?
    Are these pathways from CellSignaling, Ariadne, GeneGO, etc. ? Do you distinguish these pathways by different organisms? If yes, how can I see a particular pathway in Human, Mouse, Drosophila?
    How these pathways are connected to KEGG? How can I overlay interactions
    on these canonical pathways?

    Hope you can address these question.

    Thanks a lot!
  • BN_ January 28
    Imaging pathways are extracted from publically available pathway images (see Bioinformatics publication about this on front page) including mentioned by you.
    In the Imaging Pathways sub-tree on the left you can filter by organism.

    You can find the relation of your pathway to KEGG pathways using BuildPathwayWizard, choose intersection with canonical pathways and choose "KEGG" in the database filter.
    Again using BuildPathwayWizard you can add different types of interactions to your pathway, or a pathway constructed from your initial pathway.
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