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Instead of gene expression signatures, Kim et al. used the kinase activity profiles as the "language" for connecting kinases and small molecules in K-Map to reveal the complex interactions of kinases and inhibitors.
Focusing on ChIP-based data, instead of gene expression data, simplifies the task at hand.
For convenience, we use the term "gene" instead of "gene feature" in the microarray data descriptions.
First, we showed that using a reverse-engineering algorithm instead of gene co-expression to identify TFBS-enriched promoter sets significantly improved prediction.
It is noticeable that all significant trans effects are observed with common variants located within genes instead of gene deserts, suggesting biologically relevant interactions.
aFor uncharacterized gene targets, CpG island location was assigned instead of gene location.
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Genetic tests on bacteria, plants and animals increasingly reveal that different species crossbreed more than originally thought, meaning that instead of genes simply being passed down individual branches of the tree of life, they are also transferred between species on different evolutionary paths.
Apoptin could be delivered as an exogenous protein instead of gene-based techniques.
This is what we proposed as pathway-level consistency instead of gene-level consistency that traditional methods are based on.
For exomes, one could also further collapse entire pathways instead of genes.
Instead of gene-by-gene approaches, large sets of genes can now be addressed in a single test.
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