matrix-clustering argr

RSAT - matrix-clustering result

Analysis: argr (18/06/2026 09:35)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title argr -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.55 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/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

Download

Download

average

Ncor

Ncor = 0.55
cor = 0.6

Logo Forest (dynamic browsing)

Logo Forest (rapid overview - low image quality)

Clusters Summary

Individual Cluster View

Individual Cluster View

Show All

Hide All

cluster_1

cluster_2

cluster_3

cluster_4

Display Logo Trees

cluster_1

cluster_2

cluster_3

cluster_4

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)
Collection_1_m4_AQATSR_ArgR	AQATSR_ArgR	cluster_1	Collection_1	24	12.14	30	+++++TGAATAwwTATTCA+++++	+++++TGAATAWWTATTCA+++++
Collection_1_m12_TQGTSR_ArgR	TQGTSR_ArgR	cluster_2	Collection_1	13	9.10	4	YKhAdRnYhTdMR	YKHADRNYHTDMR
Collection_1_m7_VQPTAR_ArgR	VQPTAR_ArgR	cluster_3	Collection_1	19	17.48	20	WTMWWKATrsyATMWWKAW	WTMWWKATRSYATMWWKAW
Collection_1_m1_NQSKSR_ArgR	NQSKSR_ArgR	cluster_4	Collection_1	40	20.83	23	wrTGmATwWwwATkCAwwwwwwwTGmwTwwwwATkmwyww	WWRWKMATWWWWAWKCAWWWWWWWTGMATWWWWATKCAYW
Collection_1_m13_TQSTSR_ArgR	TQSTSR_ArgR	cluster_1	Collection_1	24	13.46	30	+++wwTgTATWwwWATAcAww+++	+++WWTGTATWWWWATACAWW+++
Collection_1_m9_TQATSR_ArgR_18bp	TQATSR_ArgR_18bp	cluster_1	Collection_1	24	10.69	316	+++wwTGwATAwwTATwCAww+++	+++WWTGWATAWWTATWCAWW+++
Collection_1_m11_SQAKSR_ArgR	SQAKSR_ArgR	cluster_1	Collection_1	24	13.99	14	+++AtTrArTAwwTAyTyAaT+++	+++ATTRARTAWWTAYTYAAT+++
Collection_1_m6_TQSSSR_ArgR	TQSSSR_ArgR	cluster_1	Collection_1	24	12.88	12	+++AWWRMATAWWTATKYWWT+++	+++awwrMATAwwTATKywwt+++
Collection_1_m14_SQSKNR_ArgR	SQSKNR_ArgR	cluster_1	Collection_1	24	16.96	12	+++wrTRAATAwwTATTYAyw+++	+++WRTRAATAWWTATTYAYW+++
Collection_1_m2_TQATSR_ArgR	TQATSR_ArgR	cluster_1	Collection_1	24	15.62	22	WWWMWTKWATWWWWATWMAWKWWW	wwwmwTkwATwwwwATwmAwkwww
Collection_1_m8_SQGTSR_ArgR	SQGTSR_ArgR	cluster_1	Collection_1	24	17.68	4	++++SYGYATAWWTATRCRS++++	++++SYGYATAWWTATRCRS++++
Collection_1_m3_SQPQSR_ArgR	SQPQSR_ArgR	cluster_1	Collection_1	24	13.34	18	+++wtTRmATAwwTATkYAaw+++	+++WTTRMATAWWTATKYAAW+++
Collection_1_m5_TQTTSR_ArgR	TQTTSR_ArgR	cluster_1	Collection_1	24	14.51	8	+++WTWGMATWWWWATKCWAW+++	+++wTWGmATWwwWATkCWAw+++
Collection_1_m10_SQSKSR_ArgR	SQSKSR_ArgR	cluster_1	Collection_1	24	11.06	102	+++wtTGmATAwwTATkCAaw+++	+++WTTGMATAWWTATKCAAW+++

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.

Heatmap View

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.

RSAT - matrix-clustering result

Analysis: argr (18/06/2026 09:35)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

Branch Motifs

Branch Motifs

Branch Motifs

Definitions

Individual Motif View

Heatmap View

Exported files