matrix-clustering citb

RSAT - matrix-clustering result

Analysis: citb (11/08/2026 09:47)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2026/08/11/matrix-clustering_2026-08-11.094700_5o2E7t/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title citb -metric_build_tree Ncor -lth w 5 -lth cor 0.4 -lth Ncor 0.3 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/08/11/matrix-clustering_2026-08-11.094700_5o2E7t/matrix-clustering

Results Summary

Nb Input motifs

Nb Input collections

Nb Clusters Found

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Root motifs

Complete results [zip]

Parameters used

Linkage method

Similarity metric

Thresholds to partition the tree

Download

Download

average

Ncor

Ncor = 0.3
cor = 0.4

Logo Forest (dynamic browsing)

Logo Forest (rapid overview - low image quality)

Clusters Summary

Individual Cluster View

Individual Cluster View

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cluster_1

Display Logo Trees

cluster_1

Display Branch-Motifs

cluster_1

Branch Motifs
Node	Consensus	Logo	Logo (Reverse)	Collections	Matrix (Transfac format)	IC	Nb sites
Node 1	-----TGAACAAAATGAACAAAA----------			Collection_1::2_motifs	PSSM	24.95	2
Node 2	-----TGAACAAAATGAACAAAA----------			Collection_1::3_motifs	PSSM	23.45	8
Node 3	-----TGAACAAAATGAACAAAA----------			Collection_1::4_motifs	PSSM	21.92	14
Node 4	-----TGAACWWWATGAACAAAA----------			Collection_1::5_motifs	PSSM	18.83	36
Node 5	-----TGAACAAAATGAACAAAA----------			Collection_1::6_motifs	PSSM	18.87	37
Node 6	-----TGAmCAAAAWGAACAAAA----------			Collection_1::7_motifs	PSSM	16.96	55
Node 7	--rttTTWTkwAAyTAAAAWAAk----------			Collection_1::2_motifs	PSSM	15.18	47
Node 8	-----TGAACAAAAwGAACAWAA----------			Collection_1::8_motifs	PSSM	16.47	65
Node 9	twAATWAAAwymATTAAAwmamTwAAAammm--			Collection_1::2_motifs	PSSM	17.84	64
Node 10	-----WGAmCAAAAwGAMCAAAAyGTCC-----			Collection_1::9_motifs	PSSM	21.32	73
Node 11	-----WGAmCAAAAwGAmCAAAAyGTCC-----			Collection_1::10_motifs	PSSM	20.22	79
Node 12	-----WGAmCAAAAwGAaCAAAAykyCC-----			Collection_1::11_motifs	PSSM	18.09	83
Node 13	twAAtTAAAwymATTAAAwmamTwAAAammaww			Collection_1::3_motifs	PSSM	17.54	72
Node 14	twawtTwwwwtaATTAAAwaAmTwAAAammaww			Collection_1::5_motifs	PSSM	16.29	119
Node 15	twawtTdAaywAAwtrAAmaAAwwAAAmmmaww			Collection_1::16_motifs	PSSM	14.10	202

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_m16_TEISQVSRK_MalR_RegPrecise	TEISQVSRK_MalR_RegPrecise	cluster_1	Collection_1	33	22.23	8	++WASTWAAWWWWYTVDTWKWYWWWTWWAWDWW	wwhWTwwAwwwrwmWAhbArwwWWTTWAsTw++
Collection_1_m15_IEVSRTTRR_CitT_RegPrecise	IEVSRTTRR_CitT_RegPrecise	cluster_1	Collection_1	33	24.95	10	+++++TTAAATCCTTTTTGTTCA++++++++++	++++++++++TGAACAAAAAGGATTTAA+++++
Collection_1_m10_AEVSRSTRR_CitT_RegPrecise	AEVSRSTRR_CitT_RegPrecise	cluster_1	Collection_1	33	24.95	1	+++++TGAACAAAATGAACAAAA++++++++++	++++++++++TTTTGTTCATTTTGTTCA+++++
Collection_1_m9_AEIARVTRR_DctR_RegPrecise	AEIARVTRR_DctR_RegPrecise	cluster_1	Collection_1	33	28.60	8	+++++GGACRTTTTGGTCTTTTTGGTCT+++++	+++++AGACCAAAAAGACCAAAAyGTCC+++++
Collection_1_m5_AEISRTTRR_CitB	AEISRTTRR_CitB	cluster_1	Collection_1	33	18.27	47	++++tTAAAwymATTAAAwmAmTwAAAammm++	++KKKTTTTWAKTKWTTTAATKRWTTTAA++++
Collection_1_m13_ATVSRATQR_CitB_RegPrecise	ATVSRATQR_CitB_RegPrecise	cluster_1	Collection_1	33	16.73	4	++++++GASYWYWRKRCAHHMWRNKC+++++++	+++++++GMnyWKddTGYMywRwrsTC++++++
Collection_1_m12_ASISRSTRR_CitT_RegPrecise	ASISRSTRR_CitT_RegPrecise	cluster_1	Collection_1	33	24.95	1	+++++TGAACAAAATGAACAAAA++++++++++	++++++++++TTTTGTTCATTTTGTTCA+++++
Collection_1_m1_AEASRTTRR_CitT	AEASRTTRR_CitT	cluster_1	Collection_1	33	18.51	22	+++++TTWTGTTCATWWWGTTCA++++++++++	++++++++++TGAACwwwATGAACAWAA+++++
Collection_1_m11_AMASRSTRR_CitT_RegPrecise	AMASRSTRR_CitT_RegPrecise	cluster_1	Collection_1	33	23.15	6	+++++TTTTGTTCATTTTGTTCA++++++++++	++++++++++TGAACAAAATGAACAAAA+++++
Collection_1_m3_TEISQVSRK_MaeM	TEISQVSRK_MaeM	cluster_1	Collection_1	33	15.48	18	++rttTTwTTaAwwTAAAAAAmk++++++++++	++++++++++MKTTTTTTAWWTTAAWAAAAY++
Collection_1_m14_IEASRTTRR_CitT_RegPrecise	IEASRTTRR_CitT_RegPrecise	cluster_1	Collection_1	33	21.35	6	+++++CTTTGCGTGATTTCTTCA++++++++++	++++++++++TGAAGAAATCACGCAAAG+++++
Collection_1_m4_ADSSKTTRR_CitB	ADSSKTTRR_CitB	cluster_1	Collection_1	33	18.22	17	twAATAAAmacCATwAAattmATAAAram++++	++++KTYTTTATKAATTTWATGGTKTTTATTWA
Collection_1_m6_TDISRVSRK_DcuR	TDISRVSRK_DcuR	cluster_1	Collection_1	33	16.34	29	+++++TTTTGTAAYTAAARWAA+++++++++++	+++++++++++TTwyTTTArTTACAAAA+++++
Collection_1_m8_AEASRTTRR_CitT_RegPrecise	AEASRTTRR_CitT_RegPrecise	cluster_1	Collection_1	33	21.51	6	+++++TTTTGTTYWTTTTGWYCA++++++++++	++++++++++TGrwCAAAAwrAACAAAA+++++
Collection_1_m2_AEIARVTRR_DctR	AEIARVTRR_DctR	cluster_1	Collection_1	33	18.94	18	+++++TTTTGKTCWTTTTGGTMT++++++++++	++++++++++akACCAAAAwGAmCAAAA+++++
Collection_1_m7_ADVSRTTRR_CitT_RegPrecise	ADVSRTTRR_CitT_RegPrecise	cluster_1	Collection_1	33	24.95	1	+++++TTTTGTTCTTTTTGTTCA++++++++++	++++++++++TGAACAAAAAGAACAAAA+++++

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: citb (11/08/2026 09:47)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

Definitions

Individual Motif View

Heatmap View

Exported files