matrix-clustering testpm

RSAT - matrix-clustering result

Analysis: testpm (17/02/2025 15:28)

Command

matrix-clustering  -v 1 -max_matrices 300 -matrix Collection_1 $RSAT/public_html/tmp/www-data/2025/02/17/matrix-clustering_2025-02-17.152816_IrspKl/matrix-clustering_query_matrices.transfac transfac -hclust_method average -calc sum -title testpm -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/2025/02/17/matrix-clustering_2025-02-17.152816_IrspKl/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

Download

Download

average

Ncor

Ncor = 0.4
cor = 0.6

Logo Forest (dynamic browsing)

Logo Forest (rapid overview - low image quality)

Clusters Summary

Individual Cluster View

Individual Cluster View

Show All

Hide All

cluster_1

cluster_2

cluster_3

Display Logo Trees

cluster_1

cluster_2

cluster_3

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)
Collection_1_m10_oligos_7nt_mkv2_m5	oligos_7nt_mkv2_m5	cluster_2	Collection_1	25	10.39	45	++++++CCYCGGRGGCTCGRGGMR+	+ykcCyCGAGCCycCgrgg++++++
Collection_1_m12_oligos_8nt_mkv2_m2	oligos_8nt_mkv2_m2	cluster_1	Collection_1	16	11.57	48	TAGGGTTAGGGTTWRG	CywAACCCTAACCCta
Collection_1_m9_oligos_7nt_mkv2_m4	oligos_7nt_mkv2_m4	cluster_1	Collection_1	16	10.57	34	++wAACCCTAACCyt+	+ARGGTTAGGGTTW++
Collection_1_m7_oligos_7nt_mkv2_m2	oligos_7nt_mkv2_m2	cluster_2	Collection_1	25	11.90	37	+++YGRHGSCTCGAGCCTYCGKGS+	+scmcGraGGCTCGAGsCdycr+++
Collection_1_m4_oligos_6nt_mkv2_m4	oligos_6nt_mkv2_m4	cluster_1	Collection_1	16	10.78	32	++wAACCCTAACCCt+	+AGGGTTAGGGTTW++
Collection_1_m11_oligos_8nt_mkv2_m1	oligos_8nt_mkv2_m1	cluster_2	Collection_1	25	10.65	63	+++++ryrcCTCGAGCCyyyrrggs	SCCYYRRRGGCTCGAGGYRY+++++
Collection_1_m13_oligos_8nt_mkv2_m3	oligos_8nt_mkv2_m3	cluster_2	Collection_1	25	9.31	49	++++++ttCCyCGAGCCyCym++++	++++KRGRGGCTCGRGGAA++++++
Collection_1_m2_oligos_6nt_mkv2_m2	oligos_6nt_mkv2_m2	cluster_2	Collection_1	25	9.66	52	+++yrrwGsCTCGAGsCtyyr++++	++++YRRAGSCTCGAGSCWYYR+++
Collection_1_m15_oligos_8nt_mkv2_m5	oligos_8nt_mkv2_m5	cluster_2	Collection_1	25	9.75	67	+++++RYGCCTCGAGCCTYYRR+++	+++yyrrAGGCTCGAGGcry+++++
Collection_1_m5_oligos_6nt_mkv2_m5	oligos_6nt_mkv2_m5	cluster_3	Collection_1	10	6.44	30	mrCCTCCGwv	BWCGGAGGYK
Collection_1_m8_oligos_7nt_mkv2_m3	oligos_7nt_mkv2_m3	cluster_2	Collection_1	25	10.78	59	+++++ryrcCTCGAGCCyyygrgg+	+CCYCRRRGGCTCGAGGYRY+++++
Collection_1_m3_oligos_6nt_mkv2_m3	oligos_6nt_mkv2_m3	cluster_2	Collection_1	25	6.88	68	+++++++++RRGGCTYGRG++++++	++++++cyCrAGCCyy+++++++++
Collection_1_m14_oligos_8nt_mkv2_m4	oligos_8nt_mkv2_m4	cluster_2	Collection_1	25	8.29	56	+++++++wyCCCaAGCCChm+++++	+++++KDGGGCTTGGGRW+++++++
Collection_1_m6_oligos_7nt_mkv2_m1	oligos_7nt_mkv2_m1	cluster_2	Collection_1	25	13.19	37	SMACRRWGSCTCGAGSCTYYGTKS+	+smacrraGsCTCGAGsCwyygtks
Collection_1_m1_oligos_6nt_mkv2_m1	oligos_6nt_mkv2_m1	cluster_2	Collection_1	25	9.83	56	+++yrraGsCTCGAGsCtyyr++++	++++YRRAGSCTCGAGSCTYYR+++

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.

RSAT - matrix-clustering result

Analysis: testpm (17/02/2025 15:28)

Command

Results Summary

Clusters Summary Table

Individual Cluster View

Branch Motifs

Branch Motifs

Branch Motifs

Definitions

Individual Motif View

Heatmap View

Exported files