RSAT - matrix-clustering result

Analysis: clustering_column-permuted_matrices_discovered_in_oct4_chip-seq (11/05/2026 05:37)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix oct4_peak_motifs_permuted $RSAT/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/matrix-clustering_query_matrices.transfac transfac -hclust_method average -calc sum -title clustering_column-permuted_matrices_discovered_in_oct4_chip-seq -metric_build_tree Ncor -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick -label_in_tree name -return json,heatmap -o $RSAT/public_html/tmp/www-data/2026/05/11/matrix-clustering_2026-05-11.053641_UD6eCh/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

21

1

17

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	2	positions_7nt_m3_perm1::oct4_peak_motifs_permuted:: positions_6nt_m2_perm1::oct4_peak_motifs_permuted::	oct4_peak_motifs_permuted::2_motifs	Show matrix
		cluster_2	2	dyads_m1_perm1::oct4_peak_motifs_permuted:: dyads_m2_perm1::oct4_peak_motifs_permuted::	oct4_peak_motifs_permuted::2_motifs	Show matrix
		cluster_3	2	local_words_6nt_m2_perm1::oct4_peak_motifs_permuted:: positions_6nt_m1_perm1::oct4_peak_motifs_permuted::	oct4_peak_motifs_permuted::2_motifs	Show matrix
		cluster_4	1	oligos_7nt_mkv5_m3_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_5	1	oligos_7nt_mkv5_m1_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_6	1	oligos_7nt_mkv5_m2_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_7	2	local_words_7nt_m3_perm1::oct4_peak_motifs_permuted:: dyads_m3_perm1::oct4_peak_motifs_permuted::	oct4_peak_motifs_permuted::2_motifs	Show matrix
		cluster_8	1	oligos_6nt_mkv4_m2_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_9	1	oligos_6nt_mkv4_m3_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_10	1	local_words_7nt_m2_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_11	1	positions_7nt_m1_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_12	1	oligos_6nt_mkv4_m1_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_13	1	local_words_7nt_m1_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_14	1	positions_7nt_m2_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_15	1	local_words_6nt_m3_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_16	1	local_words_6nt_m1_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 1 motif	Show matrix
		cluster_17	1	positions_6nt_m3_perm1::oct4_peak_motifs_permuted	oct4_peak_motifs_permuted : 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

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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

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

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)
oct4_peak_motifs_permuted_m12_oligos_7nt_mkv5_m3_perm1	oligos_7nt_mkv5_m3_perm1	cluster_4	oct4_peak_motifs_permuted	12	9.84	839	TATArrArAmrm	KYKTYTYYTATA
oct4_peak_motifs_permuted_m13_local_words_7nt_m1_perm1	local_words_7nt_m1_perm1	cluster_13	oct4_peak_motifs_permuted	19	10.00	1033	TwAyyTAwaTTTGwgyTAG	CTARCWCAAATWTARRTWA
oct4_peak_motifs_permuted_m18_positions_7nt_m3_perm1	positions_7nt_m3_perm1	cluster_1	oct4_peak_motifs_permuted	11	10.95	3939	aAAAaAAAAAA	TTTTTTTTTTT
oct4_peak_motifs_permuted_m8_positions_6nt_m2_perm1	positions_6nt_m2_perm1	cluster_1	oct4_peak_motifs_permuted	11	7.87	287	AwAAwAatwA+	+TWATTWTTWT
oct4_peak_motifs_permuted_m21_dyads_m3_perm1	dyads_m3_perm1	cluster_7	oct4_peak_motifs_permuted	16	12.03	269	++ACcsgTAAwTAwaT	ATWTAWTTACSGGT++
oct4_peak_motifs_permuted_m2_oligos_6nt_mkv4_m2_perm1	oligos_6nt_mkv4_m2_perm1	cluster_8	oct4_peak_motifs_permuted	10	7.80	992	TCysAsrGCG	CGCYSTSRGA
oct4_peak_motifs_permuted_m1_oligos_6nt_mkv4_m1_perm1	oligos_6nt_mkv4_m1_perm1	cluster_12	oct4_peak_motifs_permuted	13	9.38	2192	TwbTYwKhgTwWA	TWWACDMWRAVWA
oct4_peak_motifs_permuted_m7_positions_6nt_m1_perm1	positions_6nt_m1_perm1	cluster_3	oct4_peak_motifs_permuted	19	10.08	1428	++++ghTtcGTwTwCtWAA	TTWAGWAWACGAADC++++
oct4_peak_motifs_permuted_m4_local_words_6nt_m1_perm1	local_words_6nt_m1_perm1	cluster_16	oct4_peak_motifs_permuted	19	10.15	1028	TyTcwkAGTwTwtTwwcGA	TCGWWAAWAWACTMWGARA
oct4_peak_motifs_permuted_m3_oligos_6nt_mkv4_m3_perm1	oligos_6nt_mkv4_m3_perm1	cluster_9	oct4_peak_motifs_permuted	10	8.62	1974	rTmACCGyGk	MCRCGGTKAY
oct4_peak_motifs_permuted_m17_positions_7nt_m2_perm1	positions_7nt_m2_perm1	cluster_14	oct4_peak_motifs_permuted	21	13.24	223	AATTyArrGTTGyGyCCAwyA	TRWTGGRCRCAACYYTRAATT
oct4_peak_motifs_permuted_m9_positions_6nt_m3_perm1	positions_6nt_m3_perm1	cluster_17	oct4_peak_motifs_permuted	19	12.69	157	yryArGTTCGATCCrTwTA	TAWAYGGATCGAACYTRYR
oct4_peak_motifs_permuted_m16_positions_7nt_m1_perm1	positions_7nt_m1_perm1	cluster_11	oct4_peak_motifs_permuted	19	12.71	729	GGwTtWAwTTwAGrAyyCT	AGRRTYCTWAAWTWAAWCC
oct4_peak_motifs_permuted_m11_oligos_7nt_mkv5_m2_perm1	oligos_7nt_mkv5_m2_perm1	cluster_6	oct4_peak_motifs_permuted	11	8.79	3774	GAtwkwAAywT	AWRTTWMWATC
oct4_peak_motifs_permuted_m5_local_words_6nt_m2_perm1	local_words_6nt_m2_perm1	cluster_3	oct4_peak_motifs_permuted	19	10.07	769	CCtwrrTTwgTwAAmawAA	TTWTKTTWACWAAYYWAGG
oct4_peak_motifs_permuted_m19_dyads_m1_perm1	dyads_m1_perm1	cluster_2	oct4_peak_motifs_permuted	14	11.96	604	CCGGCssCgcCccC	GGGGGCGSSGCCGG
oct4_peak_motifs_permuted_m15_local_words_7nt_m3_perm1	local_words_7nt_m3_perm1	cluster_7	oct4_peak_motifs_permuted	16	9.51	807	TCAyGGrTgAcTAC++	++GTAGTCAYCCRTGA
oct4_peak_motifs_permuted_m20_dyads_m2_perm1	dyads_m2_perm1	cluster_2	oct4_peak_motifs_permuted	14	13.37	435	+CcACmCCcCCCCC	GGGGGGGGKGTGG+
oct4_peak_motifs_permuted_m14_local_words_7nt_m2_perm1	local_words_7nt_m2_perm1	cluster_10	oct4_peak_motifs_permuted	19	10.25	1368	ywCCTTarATvAwAcwTAr	YTAWGTWTBATYTAAGGWR
oct4_peak_motifs_permuted_m6_local_words_6nt_m3_perm1	local_words_6nt_m3_perm1	cluster_15	oct4_peak_motifs_permuted	12	8.60	1291	yGrTGTCACAry	RYTGTGACAYCR
oct4_peak_motifs_permuted_m10_oligos_7nt_mkv5_m1_perm1	oligos_7nt_mkv5_m1_perm1	cluster_5	oct4_peak_motifs_permuted	12	9.58	2583	wAwGkTwTAwRY	RYWTAWAMCWTW

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