RSAT - matrix-clustering result

Analysis: hsc_lincorr_baso (09/04/2026 19:59)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix hsc_lincorr_baso $RSAT/public_html/tmp/www-data/2026/04/09/matrix-clustering_2026-04-09.195932_t13RUQ/matrix-clustering_query_matrices.homer homer -hclust_method average -calc sum -title hsc_lincorr_baso -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/2026/04/09/matrix-clustering_2026-04-09.195932_t13RUQ/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

32

1

8

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	5	homer_26.AGATAASR::hsc_lincorr_baso:: homer_18.SAGATAAGRV::hsc_lincorr_baso:: homer_23.BBCTTATCTS::hsc_lincorr_baso:: homer_13.YCTTATCTBN::hsc_lincorr_baso:: homer_14.NBWGATAAGR::hsc_lincorr_baso::	hsc_lincorr_baso::5_motifs	Show matrix
		cluster_2	16	homer_10.MACAGGAAGT::hsc_lincorr_baso:: homer_1.ATTTCCTGTN::hsc_lincorr_baso:: homer_24.VACAGGAAAT::hsc_lincorr_baso:: homer_16.AVCCGGAAGT::hsc_lincorr_baso:: homer_3.AACCGGAAGT::hsc_lincorr_baso:: homer_5.RACCGGAAGT::hsc_lincorr_baso:: homer_11.ACTTCCKGKT::hsc_lincorr_baso:: homer_28.AVCAGGAAGT::hsc_lincorr_baso:: homer_12.ACVAGGAAGT::hsc_lincorr_baso:: homer_17.ANCAGGAAGT::hsc_lincorr_baso:: homer_7.NNAYTTCCTGHN::hsc_lincorr_baso:: homer_6.AGAGGAAGTG::hsc_lincorr_baso:: homer_4.ACAGGAAGTG::hsc_lincorr_baso:: homer_8.ACAGGAAGTG::hsc_lincorr_baso:: homer_2.ACCGGAAGTG::hsc_lincorr_baso:: homer_9.NRYTTCCGGH::hsc_lincorr_baso::	hsc_lincorr_baso::16_motifs	Show matrix
		cluster_3	3	homer_27.YGGCCCCGCCCC::hsc_lincorr_baso:: homer_25.RGKGGGCGKGGC::hsc_lincorr_baso:: homer_29.RGKGGGCGGAGC::hsc_lincorr_baso::	hsc_lincorr_baso::3_motifs	Show matrix
		cluster_4	3	homer_30.AWWWTGCTGAGTCAT::hsc_lincorr_baso:: homer_19.TGCTGAGTCA::hsc_lincorr_baso:: homer_32.VTGACTCATC::hsc_lincorr_baso::	hsc_lincorr_baso::3_motifs	Show matrix
		cluster_5	2	homer_15.TGGCAGTTGG::hsc_lincorr_baso:: homer_21.GGCVGTTR::hsc_lincorr_baso::	hsc_lincorr_baso::2_motifs	Show matrix
		cluster_6	1	homer_31.CAAAGGTCAG::hsc_lincorr_baso	hsc_lincorr_baso : 1 motif	Show matrix
		cluster_7	1	homer_20.GCTATTTTTAGC::hsc_lincorr_baso	hsc_lincorr_baso : 1 motif	Show matrix
		cluster_8	1	homer_22.CYTGGCABNSTGCCAR::hsc_lincorr_baso	hsc_lincorr_baso : 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

Display Logo Trees

cluster_1

cluster_2

cluster_3

cluster_4

cluster_5

cluster_6

cluster_7

cluster_8

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)
hsc_lincorr_baso_m23_homer_23.BBCTTATCTS	homer_23.BBCTTATCTS	cluster_1	hsc_lincorr_baso	11	8.78	101	+SWGATAAGRR	yyCTTATCWs+
hsc_lincorr_baso_m26_homer_26.AGATAASR	homer_26.AGATAASR	cluster_1	hsc_lincorr_baso	11	6.29	101	++YSTTATCW+	+wGATAAsr++
hsc_lincorr_baso_m27_homer_27.YGGCCCCGCCCC	homer_27.YGGCCCCGCCCC	cluster_3	hsc_lincorr_baso	14	9.50	100	++GGGGCGGGRCYR	yrGyCCCGCCCc++
hsc_lincorr_baso_m11_homer_11.ACTTCCKGKT	homer_11.ACTTCCKGKT	cluster_2	hsc_lincorr_baso	12	6.59	101	AASMGGAAGT++	++aCTTCCkstt
hsc_lincorr_baso_m19_homer_19.TGCTGAGTCA	homer_19.TGCTGAGTCA	cluster_4	hsc_lincorr_baso	15	9.89	100	++++tGCTGAsTCA+	+TGASTCAGCA++++
hsc_lincorr_baso_m4_homer_4.ACAGGAAGTG	homer_4.ACAGGAAGTG	cluster_2	hsc_lincorr_baso	12	9.14	100	+rCMGGAAGTg+	+CACTTCCKGY+
hsc_lincorr_baso_m17_homer_17.ANCAGGAAGT	homer_17.ANCAGGAAGT	cluster_2	hsc_lincorr_baso	12	8.99	100	AmvAGGAAGT++	++ACTTCCTBKT
hsc_lincorr_baso_m25_homer_25.RGKGGGCGKGGC	homer_25.RGKGGGCGKGGC	cluster_3	hsc_lincorr_baso	14	8.72	101	rGkGGGcGkGgc++	++GCCMCGCCCMCY
hsc_lincorr_baso_m29_homer_29.RGKGGGCGGAGC	homer_29.RGKGGGCGGAGC	cluster_3	hsc_lincorr_baso	14	10.35	100	rGkGGGCGGrGC++	++GCYCCGCCCMCY
hsc_lincorr_baso_m28_homer_28.AVCAGGAAGT	homer_28.AVCAGGAAGT	cluster_2	hsc_lincorr_baso	12	8.05	100	acvmGGAARt++	++AYTTCCKBGT
hsc_lincorr_baso_m8_homer_8.ACAGGAAGTG	homer_8.ACAGGAAGTG	cluster_2	hsc_lincorr_baso	12	8.80	101	+aCAGGAAryr+	+YRYTTCCTGT+
hsc_lincorr_baso_m16_homer_16.AVCCGGAAGT	homer_16.AVCCGGAAGT	cluster_2	hsc_lincorr_baso	12	7.73	101	ACTTCCGGBT++	++avCCGGAAGt
hsc_lincorr_baso_m24_homer_24.VACAGGAAAT	homer_24.VACAGGAAAT	cluster_2	hsc_lincorr_baso	12	9.84	101	aaCAGGAArY++	++RYTTCCTGTT
hsc_lincorr_baso_m15_homer_15.TGGCAGTTGG	homer_15.TGGCAGTTGG	cluster_5	hsc_lincorr_baso	10	7.93	101	tGrCaGTTrg	CYAACTGYCA
hsc_lincorr_baso_m9_homer_9.NRYTTCCGGH	homer_9.NRYTTCCGGH	cluster_2	hsc_lincorr_baso	12	4.12	101	+RSMGGAARYG+	+crytTCCksy+
hsc_lincorr_baso_m12_homer_12.ACVAGGAAGT	homer_12.ACVAGGAAGT	cluster_2	hsc_lincorr_baso	12	8.80	101	AyvmGGAAGT++	++ACTTCCKBRT
hsc_lincorr_baso_m2_homer_2.ACCGGAAGTG	homer_2.ACCGGAAGTG	cluster_2	hsc_lincorr_baso	12	5.73	101	+rCCGGAAGyg+	+CRCTTCCGGY+
hsc_lincorr_baso_m10_homer_10.MACAGGAAGT	homer_10.MACAGGAAGT	cluster_2	hsc_lincorr_baso	12	9.84	100	RYTTCCTGTK++	++mACAGGAARY
hsc_lincorr_baso_m21_homer_21.GGCVGTTR	homer_21.GGCVGTTR	cluster_5	hsc_lincorr_baso	10	7.90	100	+GgCvGTTr+	+YAACBGCC+
hsc_lincorr_baso_m22_homer_22.CYTGGCABNSTGCCAR	homer_22.CYTGGCABNSTGCCAR	cluster_8	hsc_lincorr_baso	16	9.50	101	cyTGGCwswswGCCAr	YTGGCWSWSWGCCARG
hsc_lincorr_baso_m6_homer_6.AGAGGAAGTG	homer_6.AGAGGAAGTG	cluster_2	hsc_lincorr_baso	12	10.48	100	+aGAGGAAGTG+	+CACTTCCTCT+
hsc_lincorr_baso_m5_homer_5.RACCGGAAGT	homer_5.RACCGGAAGT	cluster_2	hsc_lincorr_baso	12	5.90	101	arCmGGAAGt++	++ACTTCCKGYT
hsc_lincorr_baso_m3_homer_3.AACCGGAAGT	homer_3.AACCGGAAGT	cluster_2	hsc_lincorr_baso	12	6.92	101	aaCmGGAAGt++	++ACTTCCKGTT
hsc_lincorr_baso_m18_homer_18.SAGATAAGRV	homer_18.SAGATAAGRV	cluster_1	hsc_lincorr_baso	11	9.06	100	+sWGATAAGrv	BYCTTATCWS+
hsc_lincorr_baso_m7_homer_7.NNAYTTCCTGHN	homer_7.NNAYTTCCTGHN	cluster_2	hsc_lincorr_baso	12	6.22	101	VRCMGGAWRYRS	syryWTCCkgyb
hsc_lincorr_baso_m14_homer_14.NBWGATAAGR	homer_14.NBWGATAAGR	cluster_1	hsc_lincorr_baso	11	7.48	100	vswGATAAsr+	+YSTTATCWSB
hsc_lincorr_baso_m20_homer_20.GCTATTTTTAGC	homer_20.GCTATTTTTAGC	cluster_7	hsc_lincorr_baso	12	8.59	101	kCTATTTwTrGc	GCYAWAAATAGM
hsc_lincorr_baso_m13_homer_13.YCTTATCTBN	homer_13.YCTTATCTBN	cluster_1	hsc_lincorr_baso	11	7.07	101	VSWGATAAGR+	+yCTTATCwsb
hsc_lincorr_baso_m31_homer_31.CAAAGGTCAG	homer_31.CAAAGGTCAG	cluster_6	hsc_lincorr_baso	10	8.29	101	CmRAGGtCAs	STGACCTYKG
hsc_lincorr_baso_m1_homer_1.ATTTCCTGTN	homer_1.ATTTCCTGTN	cluster_2	hsc_lincorr_baso	12	9.66	101	SRCAGGAAAT++	++ATTTCCTGys
hsc_lincorr_baso_m32_homer_32.VTGACTCATC	homer_32.VTGACTCATC	cluster_4	hsc_lincorr_baso	15	8.59	101	+++++GMTGASTCAB	vTGAsTCAkc+++++
hsc_lincorr_baso_m30_homer_30.AWWWTGCTGAGTCAT	homer_30.AWWWTGCTGAGTCAT	cluster_4	hsc_lincorr_baso	15	9.87	101	ATGACTCAGCAWWWW	wwwwTGCTGAGTCAT

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