RSAT - matrix-clustering result

Analysis: tcp4_cluster_2 (16/09/2025 17:43)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix 2 $RSAT/public_html/tmp/www-data/2025/09/16/matrix-clustering_2025-09-16.174312_p9aYjS/matrix-clustering_query_matrices.transfac transfac -hclust_method average -calc sum -title tcp4_cluster_2 -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/2025/09/16/matrix-clustering_2025-09-16.174312_p9aYjS/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

12

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	8	assembly_3::2:: assembly_7::2:: assembly_19::2:: assembly_6::2:: assembly_2::2:: assembly_5::2:: assembly_4::2:: assembly_9::2::	2::8_motifs	Show matrix
		cluster_2	2	assembly_10::2:: assembly_16::2::	2::2_motifs	Show matrix
		cluster_3	1	assembly_15::2	2 : 1 motif	Show matrix
		cluster_4	1	assembly_20::2	2 : 1 motif	Show matrix
		cluster_5	1	assembly_18::2	2 : 1 motif	Show matrix
		cluster_6	1	assembly_12::2	2 : 1 motif	Show matrix
		cluster_7	1	assembly_1::2	2 : 1 motif	Show matrix
		cluster_8	1	assembly_8::2	2 : 1 motif	Show matrix
		cluster_9	1	assembly_11::2	2 : 1 motif	Show matrix
		cluster_10	1	assembly_14::2	2 : 1 motif	Show matrix
		cluster_11	1	assembly_17::2	2 : 1 motif	Show matrix
		cluster_12	1	assembly_13::2	2 : 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

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

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)
2_m9_assembly_9	assembly_9	cluster_1	2	16	7.12	1557	wwTTCAAGAAmww+++	+++WWKTTCTTGAAWW
2_m1_assembly_1	assembly_1	cluster_7	2	15	8.45	354	aaacAGAGAGAcTww	WWAGTCTCTCTGTTT
2_m5_assembly_5	assembly_5	cluster_1	2	16	8.93	263	waAgcAAGAAGAcwa+	+TWGTCTTCTTGCTTW
2_m4_assembly_4	assembly_4	cluster_1	2	16	8.41	272	DWTTCAAGAAGCTWW+	+wwAGCTTCTTGAAwh
2_m18_assembly_18	assembly_18	cluster_5	2	11	6.31	1344	wwAACAGCTww	WWAGCTGTTWW
2_m16_assembly_16	assembly_16	cluster_2	2	11	6.23	891	wwTGCAGCAww	WWTGCTGCAWW
2_m10_assembly_10	assembly_10	cluster_2	2	11	6.34	1875	waAGCAACAww	WWTGTTGCTTW
2_m17_assembly_17	assembly_17	cluster_11	2	10	8.61	169	waACGAACww	WWGTTCGTTW
2_m14_assembly_14	assembly_14	cluster_10	2	12	7.73	204	ywTCAACGCCww	WWGGCGTTGAWR
2_m6_assembly_6	assembly_6	cluster_1	2	16	8.10	459	wwTTcAAGAAGmAraw	WTYTKCTTCTTGAAWW
2_m19_assembly_19	assembly_19	cluster_1	2	16	8.23	795	wwTTcAAGAAGAAmww	WWKTTCTTCTTGAAWW
2_m7_assembly_7	assembly_7	cluster_1	2	16	7.83	525	+++WWGAGAAGACAW+	+wtgTCTTCTCww+++
2_m13_assembly_13	assembly_13	cluster_12	2	10	8.69	201	rwGGAGGAdd	HHTCCTCCWY
2_m15_assembly_15	assembly_15	cluster_3	2	11	6.43	621	wmACGTGGCww	WWGCCACGTKW
2_m8_assembly_8	assembly_8	cluster_8	2	10	8.60	524	waATGAGAww	WWTCTCATTW
2_m11_assembly_11	assembly_11	cluster_9	2	10	8.46	76	rrCGGCGAkd	HMTCGCCGYY
2_m2_assembly_2	assembly_2	cluster_1	2	16	8.38	474	wwtTCAAGAAGAmaw+	+WTKTCTTCTTGAAWW
2_m12_assembly_12	assembly_12	cluster_6	2	10	8.59	289	wtCTTCACww	WWGTGAAGAW
2_m3_assembly_3	assembly_3	cluster_1	2	16	7.45	479	+wwamCAGAAGAcww+	+WWGTCTTCTGKTWW+
2_m20_assembly_20	assembly_20	cluster_4	2	10	8.57	277	wwCTTGGAww	WWTCCAAGWW

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