RSAT - matrix-clustering result

Analysis: sva (15/03/2025 18:35)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2025/03/15/matrix-clustering_2025-03-15.183458_7qDZj4/matrix-clustering_query_matrices.tab tab -hclust_method average -calc sum -title sva -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/2025/03/15/matrix-clustering_2025-03-15.183458_7qDZj4/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

20

1

11

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	6	matrix-clustering_query_matrices.tab_4::Collection_1:: matrix-clustering_query_matrices.tab_5::Collection_1:: matrix-clustering_query_matrices.tab_8::Collection_1:: matrix-clustering_query_matrices.tab_7::Collection_1:: matrix-clustering_query_matrices.tab_15::Collection_1:: matrix-clustering_query_matrices.tab_1::Collection_1::	Collection_1::6_motifs	Show matrix
		cluster_2	2	matrix-clustering_query_matrices.tab_14::Collection_1:: matrix-clustering_query_matrices.tab_17::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_3	2	matrix-clustering_query_matrices.tab_11::Collection_1:: matrix-clustering_query_matrices.tab_2::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_4	2	matrix-clustering_query_matrices.tab_3::Collection_1:: matrix-clustering_query_matrices.tab_6::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_5	1	matrix-clustering_query_matrices.tab_19::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_6	2	matrix-clustering_query_matrices.tab_16::Collection_1:: matrix-clustering_query_matrices.tab_18::Collection_1::	Collection_1::2_motifs	Show matrix
		cluster_7	1	matrix-clustering_query_matrices.tab_10::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_8	1	matrix-clustering_query_matrices.tab_20::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_9	1	matrix-clustering_query_matrices.tab_12::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_10	1	matrix-clustering_query_matrices.tab_13::Collection_1	Collection_1 : 1 motif	Show matrix
		cluster_11	1	matrix-clustering_query_matrices.tab_9::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

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

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_m15_matrix-clustering_query_matrices.tab_15	matrix-clustering_query_matrices.tab_15	cluster_1	Collection_1	19	14.67	554	AAMAAAAWAAAAWRWAWMM	kkwTwywTTTTwTTTTkTT
Collection_1_m2_matrix-clustering_query_matrices.tab_2	matrix-clustering_query_matrices.tab_2	cluster_3	Collection_1	13	11.77	4037	ysCCTCTGCCysg	CSRGGCAGAGGSR
Collection_1_m3_matrix-clustering_query_matrices.tab_3	matrix-clustering_query_matrices.tab_3	cluster_4	Collection_1	13	11.91	1895	sGCTCCTCAC+++	+++GTGAGGAGCS
Collection_1_m1_matrix-clustering_query_matrices.tab_1	matrix-clustering_query_matrices.tab_1	cluster_1	Collection_1	19	14.06	804	AAAAAAAwAAAAwrwAwwa	TWWTWYWTTTTWTTTTTTT
Collection_1_m13_matrix-clustering_query_matrices.tab_13	matrix-clustering_query_matrices.tab_13	cluster_10	Collection_1	10	8.95	14	aaATATATtt	AAATATATTT
Collection_1_m8_matrix-clustering_query_matrices.tab_8	matrix-clustering_query_matrices.tab_8	cluster_1	Collection_1	19	15.98	4138	AAAAAAAAAAAAAA+++++	+++++TTTTTTTTTTTTTT
Collection_1_m6_matrix-clustering_query_matrices.tab_6	matrix-clustering_query_matrices.tab_6	cluster_4	Collection_1	13	10.71	4811	++CwCCTCmCTyC	GRAGKGAGGWG++
Collection_1_m18_matrix-clustering_query_matrices.tab_18	matrix-clustering_query_matrices.tab_18	cluster_6	Collection_1	12	10.16	348	YGGGAGGCCR++	++ygGCCTCCCr
Collection_1_m17_matrix-clustering_query_matrices.tab_17	matrix-clustering_query_matrices.tab_17	cluster_2	Collection_1	11	8.82	368	mmAAGAATkak	MTMATTCTTKK
Collection_1_m12_matrix-clustering_query_matrices.tab_12	matrix-clustering_query_matrices.tab_12	cluster_9	Collection_1	10	11.22	173	GTAGACATGG	CCATGTCTAC
Collection_1_m7_matrix-clustering_query_matrices.tab_7	matrix-clustering_query_matrices.tab_7	cluster_1	Collection_1	19	12.69	164	WTAAAWWWATTWTTTTWWW	wwwAAAAwAAtWwwTTTaw
Collection_1_m20_matrix-clustering_query_matrices.tab_20	matrix-clustering_query_matrices.tab_20	cluster_8	Collection_1	10	10.42	465	mkCACATCyy	RRGATGTGMK
Collection_1_m10_matrix-clustering_query_matrices.tab_10	matrix-clustering_query_matrices.tab_10	cluster_7	Collection_1	11	7.89	695	gaCACTGCAvm	KBTGCAGTGTC
Collection_1_m5_matrix-clustering_query_matrices.tab_5	matrix-clustering_query_matrices.tab_5	cluster_1	Collection_1	19	10.30	811	AWAAAAAWAAWWMW+++++	+++++wkWwTTwTTTTTwt
Collection_1_m9_matrix-clustering_query_matrices.tab_9	matrix-clustering_query_matrices.tab_9	cluster_11	Collection_1	13	11.43	225	srkCyGAGATsws	SWSATCTCRGMYS
Collection_1_m14_matrix-clustering_query_matrices.tab_14	matrix-clustering_query_matrices.tab_14	cluster_2	Collection_1	11	8.14	1106	aaAAAAATTaa	TTAATTTTTTT
Collection_1_m19_matrix-clustering_query_matrices.tab_19	matrix-clustering_query_matrices.tab_19	cluster_5	Collection_1	11	8.35	138	AgAATTATsaa	TTSATAATTCT
Collection_1_m16_matrix-clustering_query_matrices.tab_16	matrix-clustering_query_matrices.tab_16	cluster_6	Collection_1	12	9.51	402	++vsAGGCTGsa	TSCAGCCTSB++
Collection_1_m4_matrix-clustering_query_matrices.tab_4	matrix-clustering_query_matrices.tab_4	cluster_1	Collection_1	19	11.14	234	+++WWAAAWWTAWWTTTWW	wwaAAwWTAWwTTtww+++
Collection_1_m11_matrix-clustering_query_matrices.tab_11	matrix-clustering_query_matrices.tab_11	cluster_3	Collection_1	13	9.31	2672	WCCSTCTCCCY++	++rgGGAGAsGGw

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