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NCATS-Tangerine / cq-notebooks

Notebooks for answering competency questions
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Create BlueQ1: Characterization of a disease by data driven gene ontologies #10

Closed michaelkyu closed 7 years ago

michaelkyu commented 7 years ago

Input: A small set of genes that are known to be related to a disease.

Outputs:

  1. A larger set of genes that are functionally related to the input set of genes. Functional relation is determined by 'omics data, such as protein-protein interactions, genetic interactions, and co-expression.
  2. A data-driven gene ontology that organizes these genes into a hierarchy of cellular components and pathways
  3. Interactive visualization of the ontology

Example We applied this strategy to study the disease Fanconi Anemia (FA). Based on 20 genes that are known to be related to FA, we identified an additional 97 genes that are functionally related and organized these genes into a hierarchy of 25 cellular components and processes. This hierarchy and the genes can be found on the NDEx database: http://ndexbio.org/#/newNetwork/ab9bb6de-081a-11e7-aba2-0ac135e8bacf