RSAT - matrix-clustering result

Analysis: arac2 (20/01/2026 14:33)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2026/01/20/matrix-clustering_2026-01-20.143317_wUMQ9x/matrix-clustering_query_matrices.meme meme -hclust_method average -calc sum -title arac2 -metric_build_tree Ncor -lth w 10 -lth cor 0.7 -lth Ncor 0.55 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/01/20/matrix-clustering_2026-01-20.143317_wUMQ9x/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

28

1

21

average

Ncor

Ncor = 0.55
cor = 0.7

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	4	GSIYRPFYSK_HTCS_Rgu-2::Collection_1:: GTVYKPFYSK_HTCS_Rgu-2::Collection_1:: GTVYRPFYSK_HTCS_Rgu-2::Collection_1:: GTVYKPYYSK_HTCS_Rgu-2::Collection_1::	Collection_1::4_motifs	Show matrix
		cluster_2	2	SVQYRPSYAK_HTCS_Fru::Collection_1:: SVQYRPSYTK_HTCS_Fru::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_3	2	SSLNKPKYAR_HTCS_Ara-1::Collection_1:: SSLNKPKYTR_HTCS_Ara-1::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_4	2	PRTHRSNHST_RhaS::Collection_1:: PRTNRSNYSS_RhaS::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_5	2	SSNHLSSYAT_HTCS_Hep::Collection_1:: SSNHLPSYAT_HTCS_Hep::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_6	1	SSRSHQLYSR_AraC::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_7	1	SSRAHQLYSR_AraC::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_8	1	GVQYRPSYTR_HTCS_Fru::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_9	1	SSVFKPRYSK_HTCS_Rgu-1::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_10	1	SSTYRTGYRQ_HTCS_Ara-2::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_11	1	SSTYRSVYRQ_HTCS_Ara-2::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_12	1	ATNFTSRYSK_HTCS_Hya::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_13	1	SRQYRRGTYK_HTCS_Man-2::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_14	1	SRSYRKVTFK_HTCS_Man-1_3::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_15	1	SSWRKTEHFS_RhaR::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_16	1	SASYTISYST_HTCS_Ogl-2::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_17	1	SSSYRPKYAT_HTCS_Aga-1::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_18	1	SRVRQSNYSV_RhaR::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_19	1	SSTYRTVYRQ_HTCS_Ara-2::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_20	1	SKQYRHSYSK_HTCS_Pga::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_21	1	SYHHRTSYIT_AdaA::Collection_1	Collection_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

cluster_8

cluster_9

cluster_10

cluster_11

cluster_12

cluster_13

cluster_14

cluster_15

cluster_16

cluster_17

cluster_18

cluster_19

cluster_20

cluster_21

Display Logo Trees

cluster_1

cluster_2

cluster_3

cluster_4

cluster_5

cluster_6

cluster_7

cluster_8

cluster_9

cluster_10

cluster_11

cluster_12

cluster_13

cluster_14

cluster_15

cluster_16

cluster_17

cluster_18

cluster_19

cluster_20

cluster_21

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)
Collection_1_m16_SSLNKPKYTR_HTCS_Ara-1	SSLNKPKYTR_HTCS_Ara-1	cluster_3	Collection_1	30	15.85	22	wGkysrmCmwwhrarytydwwkGkysrmCw	WGKYSRMCMWWHRARYTYDWWKGKYSRMCW
Collection_1_m24_GTVYKPFYSK_HTCS_Rgu-2	GTVYKPFYSK_HTCS_Rgu-2	cluster_1	Collection_1	34	18.38	16	TRGAVWAWTKTHCAWWWWWWTGDAMAWTWBTCYA	TrgAvWAwTkThCAwwwwwwTGdAmAwTWbTcyA
Collection_1_m14_SSRAHQLYSR_AraC	SSRAHQLYSR_AraC	cluster_7	Collection_1	38	16.66	16	hdrsrkdwawdTrsmTRwwwwYAksyAhwtwhmysyhd	HDRSRKDWAWDTRSMTRWWWWYAKSYAHWTWHMYSYHD
Collection_1_m18_GTVYRPFYSK_HTCS_Rgu-2	GTVYRPFYSK_HTCS_Rgu-2	cluster_1	Collection_1	34	19.61	32	TrgAmdAwtwTmCAwwwwwwTGkAwawThkTcyA	TRGAMDAWTWTMCAWWWWWWTGKAWAWTHKTCYA
Collection_1_m7_ATNFTSRYSK_HTCS_Hya	ATNFTSRYSK_HTCS_Hya	cluster_12	Collection_1	32	13.26	24	wGwAywrTwywwwwwwwwwwwwrwAywrTwCw	WGWAYWRTWYWWWWWWWWWWWWRWAYWRTWCW
Collection_1_m23_SRVRQSNYSV_RhaR	SRVRQSNYSV_RhaR	cluster_18	Collection_1	51	48.21	3	wTCTTGAAAAAwmGACsdddddddddddddddddCGTyrAAAATTTAAGGT	ACCTTAAATTTTYRACGHHHHHHHHHHHHHHHHHSGTCKWTTTTTCAAGAW
Collection_1_m26_SSVFKPRYSK_HTCS_Rgu-1	SSVFKPRYSK_HTCS_Rgu-1	cluster_9	Collection_1	33	12.16	52	swrwAawTwywvwwwwwwwwwbwrwAwtTwyws	SWRWAAWTWYWVWWWWWWWWWBWRWAWTTWYWS
Collection_1_m15_SSTYRTVYRQ_HTCS_Ara-2	SSTYRTVYRQ_HTCS_Ara-2	cluster_19	Collection_1	32	13.86	4	wrmwmkwkywnnnnnnnnnnnnwrmwmkwkyw	WRMWMKWKYWNNNNNNNNNNNNWRMWMKWKYW
Collection_1_m8_GVQYRPSYTR_HTCS_Fru	GVQYRPSYTR_HTCS_Fru	cluster_8	Collection_1	30	13.95	4	RMAwswWdmnnnnnnnnnnnnkhWwswTKY	RMAWSWWDMNNNNNNNNNNNNKHWWSWTKY
Collection_1_m9_SSSYRPKYAT_HTCS_Aga-1	SSSYRPKYAT_HTCS_Aga-1	cluster_17	Collection_1	34	16.97	6	ykrTmwwywTTyrwwwwwwwwyrAAwrwwkAymr	YKRTMWWYWTTYRWWWWWWWWYRAAWRWWKAYMR
Collection_1_m2_GSIYRPFYSK_HTCS_Rgu-2	GSIYRPFYSK_HTCS_Rgu-2	cluster_1	Collection_1	34	20.78	12	TRKABWAWWRTMCAWWWWWWTGKAYWWTWVTMYA	TrkAbwAwwrTmCAwwwwwwTGkAywwTwvTmyA
Collection_1_m21_SRSYRKVTFK_HTCS_Man-1_3	SRSYRKVTFK_HTCS_Man-1_3	cluster_14	Collection_1	37	13.37	16	kkryrcwdwhrTkhmmnnnnnkkdmAydwhwgyrymm	KKRYRCWDWHRTKHMMNNNNNKKDMAYDWHWGYRYMM
Collection_1_m17_SYHHRTSYIT_AdaA	SYHHRTSYIT_AdaA	cluster_21	Collection_1	16	13.86	2	wkyrwkATmwyrmwAT	ATWKYRWKATMWYRMW
Collection_1_m13_SSLNKPKYAR_HTCS_Ara-1	SSLNKPKYAR_HTCS_Ara-1	cluster_3	Collection_1	30	24.95	2	wGkysrmCwmAwrwrywywTkwGkysrmCw	WGKYSRMCWMAWRWRYWYWTKWGKYSRMCW
Collection_1_m3_SSTYRSVYRQ_HTCS_Ara-2	SSTYRSVYRQ_HTCS_Ara-2	cluster_11	Collection_1	32	19.41	4	wbwwhdwkhwwwwwwwwwwwwwwdmwhdwwvw	WBWWHDWKHWWWWWWWWWWWWWWDMWHDWWVW
Collection_1_m5_SSWRKTEHFS_RhaR	SSWRKTEHFS_RhaR	cluster_15	Collection_1	28	22.39	5	yCAAATCaaaaaaaaaaaaaaTCAAAAa	TTTTTGATTTTTTTTTTTTTTGATTTGR
Collection_1_m20_SVQYRPSYTK_HTCS_Fru	SVQYRPSYTK_HTCS_Fru	cluster_2	Collection_1	30	13.06	26	gwwWswWwywwwwwwwwwwwwrwWwsWwwc	GWWWSWWWYWWWWWWWWWWWWRWWWSWWWC
Collection_1_m4_GTVYKPYYSK_HTCS_Rgu-2	GTVYKPYYSK_HTCS_Rgu-2	cluster_1	Collection_1	34	17.27	18	TrrAmwAwwkTmCAwwwwwwTGkAmwwTwkTyyA	TRRAMWAWWKTMCAWWWWWWTGKAMWWTWKTYYA
Collection_1_m12_SSRSHQLYSR_AraC	SSRSHQLYSR_AraC	cluster_6	Collection_1	38	13.57	39	TadsrawwkwwycsmTAwwwwTAksgrmwmwwtyshtR	YADSRAWWKWKYCSMTAWWWWTAKSGRWWMWWTYSHTA
Collection_1_m25_SKQYRHSYSK_HTCS_Pga	SKQYRHSYSK_HTCS_Pga	cluster_20	Collection_1	35	22.18	4	wymGwyykrwywTwnnnnnnnwAwrwymrrwCkrw	WYMGWYYKRWYWTWNNNNNNNWAWRWYMRRWCKRW
Collection_1_m1_SSNHLSSYAT_HTCS_Hep	SSNHLSSYAT_HTCS_Hep	cluster_5	Collection_1	31	17.36	8	wCMWATwTrdwwwwwwwwwwwhyAwATWKGw	WCMWATWTRDWWWWWWWWWWWHYAWATWKGW
Collection_1_m11_SRQYRRGTYK_HTCS_Man-2	SRQYRRGTYK_HTCS_Man-2	cluster_13	Collection_1	37	20.19	4	dkWCRhwwwhdbRdmwnnnnnwkhYvhdwwwdYGWmh	DKWCRHWWWHDBRDMWNNNNNWKHYVHDWWWDYGWMH
Collection_1_m19_PRTHRSNHST_RhaS	PRTHRSNHST_RhaS	cluster_4	Collection_1	51	26.92	20	ACCTTYvymhtwyTGCCAnnnnnnnnnnnnnnnTGGCArwadkrbRAAGGT	ACCTTYVYMHTWYTGCCANNNNNNNNNNNNNNNTGGCARWADKRBRAAGGT
Collection_1_m6_SSNHLPSYAT_HTCS_Hep	SSNHLPSYAT_HTCS_Hep	cluster_5	Collection_1	31	15.99	12	wyaAwwTTrwwwwwwwwwwwwwyAAwwTtrw	WYAAWWTTRWWWWWWWWWWWWWYAAWWTTRW
Collection_1_m10_SVQYRPSYAK_HTCS_Fru	SVQYRPSYAK_HTCS_Fru	cluster_2	Collection_1	30	11.13	12	rwwwswWwywwwwwwwwwwwwrwWwswwwy	RWWWSWWWYWWWWWWWWWWWWRWWWSWWWY
Collection_1_m22_SASYTISYST_HTCS_Ogl-2	SASYTISYST_HTCS_Ogl-2	cluster_16	Collection_1	38	29.99	4	dTTmRhrMWThwYkMWwwwwwwWKmRwdAWKydYkAAh	DTTMRHRMWTHWYKMWWWWWWWWKMRWDAWKYDYKAAH
Collection_1_m28_SSTYRTGYRQ_HTCS_Ara-2	SSTYRTGYRQ_HTCS_Ara-2	cluster_10	Collection_1	31	11.44	12	wrAwyrwtywwwwwwwwwwwwwrawyrwTyw	WRAWYRWTYWWWWWWWWWWWWWRAWYRWTYW
Collection_1_m27_PRTNRSNYSS_RhaS	PRTNRSNYSS_RhaS	cluster_4	Collection_1	51	27.67	8	wyCTTsrkhwhwmTGCCAnnnnnnnnnnnnnnnTGGCAkwdwdmysAAGrw	WYCTTSRKHWHWMTGCCANNNNNNNNNNNNNNNTGGCAKWDWDMYSAAGRW

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.

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