JASPAR CORE Fungi clustering

JASPAR profile clustering summary

Matrix (or TF binding profile) clusters simplify the biological interpretation and exploration of the numerous motifs present in our collections. Matrix clustering groups and aligns transcription factor binding motifs using hierarchical clustering with a correlation metric. These clusters are also annotated with the corresponding TF structural class information for further context.

Description of the main files:

  • Logo forest: interactive and collapsible tree visualization of the motif clustering where leaves are decorated with the aligned motifs at the current tree height.
  • Radial tree: interactive tree visualization of all the input motifs to produce a global picture of their relatedness.

Description of the additional files:

  • Pairwise comparison: a table showing the pairwise comparison between all the input motifs using different metrics. This table provides the detailed matrix comparison analysis results.
  • Pairwise comparison heatmap: heatmap visualization illustrating the pairwise similarity between all input motifs. The axes represent the individual motifs, along with coloured annotation bars indicating the motif cluster. The heatmap entries are coloured according to the level of similarity between the considered motif pair in terms of length normalized correlation.
  • Cluster table: a table containing information on the composition of the clusters and their corresponding motifs.
  • Annotation table: a table providing the structural class information about each input motif.
  • Rand index heatmap: heatmap visualization illustrating the pairwise similarity between all input motifs. The axes represent the individual motifs, along with coloured annotation bars indicating the motif cluster. The heatmap entries are coloured according to the level of similarity between the considered motif pair in terms of length normalized correlation.