Data harvested and integrated from the following resources form the backbone of oncoEnrichR:
This section describes the underlying annotation types of oncoEnrichR in detail, and to what extent they are subject to quality control/filtering for use within the package.
We assign three confidence levels with respect to genes having oncogenic and/or tumor suppressive roles
Very Strong
Strong
Moderate
Literature support for a tumor suppressive role is ignored if the gene has 2.5 times as much literature support for an oncogenic role (and vice versa)
Classification of genes as potential cancer drivers require support from at least two of the following sources:
Protein-protein interactions for members of the target set is explored using data from two different resources:
STRING - a database of known and predicted protein-protein interactions, including direct (physical) and indirect (functional) associations. In oncoEnrichR, the publicly available STRING API is utilized for network retrieval, and the users have the possibility to configure the following:
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