RSAT - matrix-clustering result

Analysis: wt_top1 (30/05/2025 13:41)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix wt_top1 $RSAT/public_html/tmp/www-data/2025/05/30/matrix-clustering_2025-05-30.134052_FDIEgh/matrix-clustering_query_matrices.homer homer -hclust_method average -calc sum -title wt_top1 -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/2025/05/30/matrix-clustering_2025-05-30.134052_FDIEgh/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

22

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	3	homer_23.CACTCACCAGGG::wt_top1:: homer_14.ACACCCGCAA::wt_top1:: homer_15.CTGCCSGCAAGG::wt_top1::	wt_top1::3_motifs	Show matrix
		cluster_2	1	homer_7.GGGAAGCAGCCT::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_3	1	homer_9.RGATGGCGDCCG::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_4	2	homer_28.TGCCCCAA::wt_top1:: homer_2.TGCGCCAGAT::wt_top1::	wt_top1::2_motifs	Show matrix
		cluster_5	2	homer_10.CCYAANCCAA::wt_top1:: homer_20.TCTGGAACGGGC::wt_top1::	wt_top1::2_motifs	Show matrix
		cluster_6	2	homer_29.AGAGBGTCRCAG::wt_top1:: homer_30.GAGTCGCGGA::wt_top1::	wt_top1::2_motifs	Show matrix
		cluster_7	2	homer_25.TGCGGTAC::wt_top1:: homer_5.CGCGGAACTT::wt_top1::	wt_top1::2_motifs	Show matrix
		cluster_8	1	homer_1.GGGCACMTGYCC::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_9	1	homer_13.GTGGWCCGSAGA::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_10	2	homer_18.AGTCTTGCCC::wt_top1:: homer_31.ACGGGCGATA::wt_top1::	wt_top1::2_motifs	Show matrix
		cluster_11	2	homer_21.MAGCCTCAGCAG::wt_top1:: homer_32.CASAGSCAGAGS::wt_top1::	wt_top1::2_motifs	Show matrix
		cluster_12	3	homer_26.CTAAGACC::wt_top1:: homer_19.ATTAGTCTGA::wt_top1:: homer_24.GGACCAMGAT::wt_top1::	wt_top1::3_motifs	Show matrix
		cluster_13	1	homer_12.WCSGGACY::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_14	1	homer_27.ATAGGGAA::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_15	1	homer_22.TCTAACCTGTTC::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_16	1	homer_3.GGTRGCCKGCTK::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_17	1	homer_17.AAGCACAGTG::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_18	1	homer_6.ACCRGCKGTC::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_19	1	homer_8.ATCCCGTGTGGG::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_20	1	homer_11.GGGCCTGCACTG::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_21	1	homer_4.NGGAAMTTAGKG::wt_top1	wt_top1 : 1 motif	Show matrix
		cluster_22	1	homer_16.RCTCGAGTCKVG::wt_top1	wt_top1 : 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

cluster_22

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

cluster_22

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)
wt_top1_m29_homer_29.AGAGBGTCRCAG	homer_29.AGAGBGTCRCAG	cluster_6	wt_top1	13	12.39	100	AGAGtGTCrCAG+	+CTGYGACACTCT
wt_top1_m27_homer_27.ATAGGGAA	homer_27.ATAGGGAA	cluster_14	wt_top1	8	3.57	100	ATAGGGAA	TTCCCTAT
wt_top1_m12_homer_12.WCSGGACY	homer_12.WCSGGACY	cluster_13	wt_top1	8	7.33	100	wmsGGACy	RGTCCSKW
wt_top1_m32_homer_32.CASAGSCAGAGS	homer_32.CASAGSCAGAGS	cluster_11	wt_top1	14	3.77	101	casAgscasags++	++SCTSTGSCTSTG
wt_top1_m6_homer_6.ACCRGCKGTC	homer_6.ACCRGCKGTC	cluster_18	wt_top1	10	5.98	101	aCCrGCkGTC	GACMGCYGGT
wt_top1_m23_homer_23.CACTCACCAGGG	homer_23.CACTCACCAGGG	cluster_1	wt_top1	13	14.37	100	+CCCTGGTGRGTG	CACYCACCAGGG+
wt_top1_m9_homer_9.RGATGGCGDCCG	homer_9.RGATGGCGDCCG	cluster_3	wt_top1	12	10.69	100	rGAwGSyGrCCk	MGGYCRSCWTCY
wt_top1_m30_homer_30.GAGTCGCGGA	homer_30.GAGTCGCGGA	cluster_6	wt_top1	13	12.01	100	+++GArTCsCGGA	TCCGSGAYTC+++
wt_top1_m14_homer_14.ACACCCGCAA	homer_14.ACACCCGCAA	cluster_1	wt_top1	13	4.46	100	ACACCCGCAA+++	+++TTGCGGGTGT
wt_top1_m2_homer_2.TGCGCCAGAT	homer_2.TGCGCCAGAT	cluster_4	wt_top1	10	11.31	100	TGCGmCAGAT	ATCTGKCGCA
wt_top1_m22_homer_22.TCTAACCTGTTC	homer_22.TCTAACCTGTTC	cluster_15	wt_top1	12	6.75	101	TCTaACCTGTTC	GAACAGGTTAGA
wt_top1_m3_homer_3.GGTRGCCKGCTK	homer_3.GGTRGCCKGCTK	cluster_16	wt_top1	12	11.58	100	GkTrGCYkGCTk	MAGCMRGCYAMC
wt_top1_m4_homer_4.NGGAAMTTAGKG	homer_4.NGGAAMTTAGKG	cluster_21	wt_top1	12	3.56	101	mGGwAmwtAgkg	CMCTAWKTWCCK
wt_top1_m1_homer_1.GGGCACMTGYCC	homer_1.GGGCACMTGYCC	cluster_8	wt_top1	12	10.53	101	GGrCACmwGyCC	GGRCWKGTGYCC
wt_top1_m17_homer_17.AAGCACAGTG	homer_17.AAGCACAGTG	cluster_17	wt_top1	10	6.55	101	rrkCACwGtG	CACWGTGMYY
wt_top1_m11_homer_11.GGGCCTGCACTG	homer_11.GGGCCTGCACTG	cluster_20	wt_top1	12	10.01	101	GGGCmkGmwCTG	CAGWKCMKGCCC
wt_top1_m31_homer_31.ACGGGCGATA	homer_31.ACGGGCGATA	cluster_10	wt_top1	12	10.48	100	++TATCGCCCGT	ACGGGCGATA++
wt_top1_m28_homer_28.TGCCCCAA	homer_28.TGCCCCAA	cluster_4	wt_top1	10	3.57	100	TGCCCCAA++	++TTGGGGCA
wt_top1_m15_homer_15.CTGCCSGCAAGG	homer_15.CTGCCSGCAAGG	cluster_1	wt_top1	13	7.71	101	mkrCysGsAAGG+	+CCTTSCSRGYMK
wt_top1_m16_homer_16.RCTCGAGTCKVG	homer_16.RCTCGAGTCKVG	cluster_22	wt_top1	12	7.70	100	rCTCGASyCkvs	SBMGRSTCGAGY
wt_top1_m18_homer_18.AGTCTTGCCC	homer_18.AGTCTTGCCC	cluster_10	wt_top1	12	13.81	100	AGTCTTGCCC++	++GGGCAAGACT
wt_top1_m20_homer_20.TCTGGAACGGGC	homer_20.TCTGGAACGGGC	cluster_5	wt_top1	12	7.49	100	GCCYGTKCCAGA	TcTGGmACrGGC
wt_top1_m8_homer_8.ATCCCGTGTGGG	homer_8.ATCCCGTGTGGG	cluster_19	wt_top1	12	11.65	100	RyCCCGwGTGGr	YCCACWCGGGRY
wt_top1_m21_homer_21.MAGCCTCAGCAG	homer_21.MAGCCTCAGCAG	cluster_11	wt_top1	14	12.75	100	++mAGyCwCAGCAG	CTGCTGWGRCTK++
wt_top1_m19_homer_19.ATTAGTCTGA	homer_19.ATTAGTCTGA	cluster_12	wt_top1	13	5.16	101	++mTTrGtCygA+	+TCRGACYAAK++
wt_top1_m5_homer_5.CGCGGAACTT	homer_5.CGCGGAACTT	cluster_7	wt_top1	10	12.52	100	CGCsGAACTT	AAGTTCSGCG
wt_top1_m26_homer_26.CTAAGACC	homer_26.CTAAGACC	cluster_12	wt_top1	13	3.57	100	+++++GGTCTTAG	CTAAGACC+++++
wt_top1_m25_homer_25.TGCGGTAC	homer_25.TGCGGTAC	cluster_7	wt_top1	10	3.57	100	TGCGGTAC++	++GTACCGCA
wt_top1_m10_homer_10.CCYAANCCAA	homer_10.CCYAANCCAA	cluster_5	wt_top1	12	6.71	101	+CCyAAvCCwm+	+KWGGBTTRGG+
wt_top1_m13_homer_13.GTGGWCCGSAGA	homer_13.GTGGWCCGSAGA	cluster_9	wt_top1	12	10.05	101	GyGGdCCGsrGA	TCYSCGGHCCRC
wt_top1_m7_homer_7.GGGAAGCAGCCT	homer_7.GGGAAGCAGCCT	cluster_2	wt_top1	12	5.68	101	RGrArkcrgyCT	AGRCYGMYTYCY
wt_top1_m24_homer_24.GGACCAMGAT	homer_24.GGACCAMGAT	cluster_12	wt_top1	13	11.58	100	ATCKTRRTCC+++	+++GGAYyAmGAT

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