RSAT - matrix-clustering result

Analysis: mp (14/01/2025 20:10)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix jaspar2022_clustered $RSAT/public_html/tmp/www-data/2025/01/14/matrix-clustering_2025-01-14.140337_B3CH8J/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title mp -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick -radial_tree_only -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2025/01/14/matrix-clustering_2025-01-14.140337_B3CH8J/matrix-clustering

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

841

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