Simplify regulator-target gene network via clustering.

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Description

Several regulators (specifically TFs) might have extremely overlapping target genes. In order to identify clusters of highly similar regulators (mainly TFs) we implemented a network simplification algorithm in biRte: We construct the biadjacency matrix of the complete bipartite regulator target-gene graph and then calculate a single linkage clustering of regulators based on the Tanimoto-Jaccard similarity of their target genes. The dendrogram is cut at a defined height (default: 0.1) to idenfity resulting groups. The algorithm is meant to simplify the inference of active regulators, because the resulting regulator clusters have more dissimilar target gene profiles.

Usage

1
simplify(affinities, cutoff=0.9)

Arguments

affinities

original regulator-target gene network

cutoff

cut dendrogram at height 1 - cutoff (i.e. similarity cutoff)

Value

clustered / simplified network

Author(s)

Holger Froehlich

Examples

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