RSAT - matrix-clustering result

Analysis: JASPAR_2020_insects (07/10/2019 12:20)

Command

matrix-clustering  -v 2 -matrix JASPAR_2020_insects data/motifs/JASPAR2020_CORE_insects.tf tf -hclust_method average -calc sum -title 'JASPAR 2020 insects' -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -label_in_tree name -return json -quick -radial_tree_only -o results/JASPAR_2020_matrix_clustering/insects/radial_trees/JASPAR_2020_matrix_clustering_insects -ID_link_color_table data/annotation_tables/jaspar2020_insects_annotations_with_colours.tsv

Results Summary

Nb Input motifs

Nb Input collections

Nb Clusters Found

Download
Root motifs

Complete results [zip]

Parameters used

Linkage method

Similarity metric

Thresholds to partition the tree

143

1

1

average

Ncor

Ncor = 0.4
cor = 0.6

Radial Tree

References
1. Castro-Mondragon JA et al. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. doi: 10.1093/nar/gkx314; Nucleic Acids Research (2017)
2. Last RSAT release: Nguyen NTT et al. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research (2018).
Additional Information
- Jacques van Helden course
Contact
- Jaime Castro-Mondragon - j.a.c.mondragon@ncmm.uio.no
- Morgane Thomas-Chollier - mthomas@biologie.ens.fr
- Jacques van Helden - Jacques.van-Helden@univ-amu.fr