RSAT - matrix-clustering result

Analysis: ap2-erf_consensus-motif (14/05/2025 12:59)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 $RSAT/public_html/tmp/www-data/2025/05/14/matrix-clustering_2025-05-14.125855_oUftcg/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title ap2-erf_consensus-motif -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick -label_in_tree name -return json -o $RSAT/public_html/tmp/www-data/2025/05/14/matrix-clustering_2025-05-14.125855_oUftcg/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

7

1

7

average

Ncor

Ncor = 0.4
cor = 0.6

Logo Forest (dynamic browsing)

Logo Forest (rapid overview - low image quality)

Clusters Summary

Clusters Summary Table

Root Motif	Root Motif (Reverse)	Cluster ID	# Motifs	Motif_Name::Collection	Number of Motifs by Collection	Root Motif (transfac Format)
		cluster_1	1	MA1219.1::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix
		cluster_2	1	MA1222.1::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix
		cluster_3	1	MA1232.1::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix
		cluster_4	1	MA1233.2::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix
		cluster_5	1	MA1234.1::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix
		cluster_6	1	MA1248.1::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix
		cluster_7	1	MA1263.1::ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1 : 1 motif	Show matrix

Note: by default the table displays the first 50 clusters. Click on the Show X entries button to display more (or less) clusters.
Click on the column names to change the order of the data.
Use the Search window to find your motif (s) of interest.

Individual Cluster View

Individual Cluster View

Show All

Hide All

cluster_1

cluster_2

cluster_3

cluster_4

cluster_5

cluster_6

cluster_7

Display Logo Trees

cluster_1

cluster_2

cluster_3

cluster_4

cluster_5

cluster_6

cluster_7

Display Branch-Motifs

Each cluster has a different color.
Click on the upper buttons to display separately the information of each cluster.
Click on the circles at each tree to display its corresponding merged motifs.

Definitions

Logo tree.
This results shows the hierarchical tree with its logo alignment of one cluster.
The logos are shown in Forward (left logo) and Reverse (right logo) orientation.
Branch-motifs.
On the trees are displayed the branch number that is the number in which the motifs were incorporated in the tree.
The Branch-Motifs table shows the logo in both orientations and the link to the file in TRANSFAC format with the branch-motif.

Individual Motif View

Individual Motif View

Motif id	Motif name	Cluster	Collection	Width	IC	Number of sites	Consensus	Consensus (Rev)	Logo	Logo (Rev)
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m7_MA1263.1	MA1263.1	cluster_7	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	15	0.00	0	---------------	---------------
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m3_MA1232.1	MA1232.1	cluster_3	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	21	0.00	0	---------------------	---------------------
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m2_MA1222.1	MA1222.1	cluster_2	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	16	0.00	0	----------------	----------------
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m4_MA1233.2	MA1233.2	cluster_4	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	16	0.00	0	----------------	----------------
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m6_MA1248.1	MA1248.1	cluster_6	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	21	0.00	0	---------------------	---------------------
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m5_MA1234.1	MA1234.1	cluster_5	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	15	0.00	0	---------------	---------------
ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1_m1_MA1219.1	MA1219.1	cluster_1	ma1219.1_ma1222.1_ma1232.1_ma1233.2_ma1234.1_ma1248.1_ma1263.1	16	9.34	600	ccaycdcCACCGmCa-	-TGKCGGTGGHGRTGG

Click on the column names to change the order of the data.
Write the name of one cluster, collection or a pattern in the Search window.

Additional Files

Exported files

File	Description
Pairwise comparison	This table shows the pairwise comparison between all the input motifs using different metrics. This is the compare-matrices result.
Matrix description	This table shows information of each input motif.
Cluster-wise Motif Files [zip]	One TRANSFAC file is generated for each cluster including all the input motifs grouped in the corresponding cluster.
Root motifs	A file with the root matrix of each cluster.
Motif collections per cluster	A tab separated file containing the counts of motif of each collection on each cluster.
Clusters	A tab separated file containing the clusters and their correspondng motifs.
Central motifs IDs	A tab separated file containing the central motif, that one who is the most similar to all the others motif in the same cluster.
Central motifs (in TRANSFAC format)	A transfac file containing the central motif, that one who is the most similar to all the others motif within the same cluster.
Input motifs	The input motifs analyzed with matrix-clustering.

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