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Caleydo facilitates a deeper understanding of the biological effects of altered gene expression in disease conditions across pathway boundaries.
Our contribution enables seamless interaction in a visual environment across pathway databases (currently, KEGG and BioCarta), and the simultaneous display of linked gene expression profiles.
A further related question concerns the validity of the criteria used by the collators to assess relative inter-areal connection strengths (including apparent 'absences') across pathway tracing experiments that used techniques with differing sensitivities.
Further, the concordance of our learned interaction sign and the interaction sign in databases, despite the various ways that interaction sign is annotated in the BioPAX language across pathway databases, indicates that pathway databases have successfully and faithfully cataloged of thousands of wetlab experiments in the literature.
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This information allows us to answer general questions on the structural anatomy of the SMM pathway proteins and to trace family relationships and recruitment events within and across pathways.
Signal transduction pathways that terminate in TF activation are non-linear, with cross-talk at multiple levels that affects activity across pathways [5], [6], [7].
Given the limited size of this data set, this modeling exercise was performed to explore potential combinations within or across pathways that might form the basis of future studies.
Collective testing of genes across pathways addresses this possibility.
Interestingly, ME associations are typically expected within a pathway and not across pathways [ 11].
Chemicals ranged in promiscuity across pathways, from no activity to affecting dozens of pathways.
DAVID tests the null hypothesis that genes are uniformly distributed across pathways and biologic functions.
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