# RSAT - matrix-clustering result

### Analysis: tcp4_cluster_1 (16/09/2025 10:22)

## 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 | 13 | Download | Download |
average | Ncor | Ncor = 0.4 cor = 0.6

| Logo Forest (dynamic browsing) Logo Forest (rapid overview - low image quality) 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
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 | assembly_12::Collection_1:: assembly_13::Collection_1:: assembly_7::Collection_1:: | Collection_1::3_motifs | Show matrix
|  | cluster_2 | 3 | assembly_15::Collection_1:: assembly_10::Collection_1:: assembly_1::Collection_1:: | Collection_1::3_motifs | Show matrix
|  | cluster_3 | 3 | assembly_2::Collection_1:: assembly_3::Collection_1:: assembly_4::Collection_1:: | Collection_1::3_motifs | Show matrix
|  | cluster_4 | 1 | assembly_14::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_5 | 1 | assembly_16::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_6 | 2 | assembly_6::Collection_1:: assembly_9::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_7 | 1 | assembly_17::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_8 | 1 | assembly_8::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_9 | 1 | assembly_18::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_10 | 1 | assembly_19::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_11 | 1 | assembly_5::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_12 | 1 | assembly_20::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_13 | 1 | assembly_11::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
cluster_12
cluster_13
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
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w k g A G C T T C C w w |  |  | Collection_1::2_motifs | PSSM | 8.11 | 257
Node 2 | w w w r A G M T T C y w w |  |  | Collection_1::3_motifs | PSSM | 7.50 | 877

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | r w r r c A G A G A G A s w r |  |  | Collection_1::2_motifs | PSSM | 7.93 | 1441
Node 2 | r w r r m a G A s A G A a a a |  |  | Collection_1::3_motifs | PSSM | 6.51 | 4123

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -w w T s A A G A A G A A r a r r a |  |  | Collection_1::2_motifs | PSSM | 7.90 | 2735
Node 2 | w w w t s A A G A A G A A r a r a a |  |  | Collection_1::3_motifs | PSSM | 7.37 | 3054

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A G A A A G w w |  |  | Collection_1 : 1 motif | PSSM | 8.76 | 951

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C A A A A G w w |  |  | Collection_1 : 1 motif | PSSM | 8.61 | 1043

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w a A g a A r C A G C A G m a w w |  |  | Collection_1::2_motifs | PSSM | 7.60 | 745

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A G G A C A w d |  |  | Collection_1 : 1 motif | PSSM | 8.62 | 263

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A C C A C A A w w |  |  | Collection_1 : 1 motif | PSSM | 6.45 | 3312

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w T C T G A G A w w |  |  | Collection_1 : 1 motif | PSSM | 6.29 | 2159

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w t C T G C A A w w |  |  | Collection_1 : 1 motif | PSSM | 8.62 | 326

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | h d C C G G C G A w w |  |  | Collection_1 : 1 motif | PSSM | 6.25 | 412

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w T C A A G A C w w |  |  | Collection_1 : 1 motif | PSSM | 6.36 | 2293

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w T G A G C T G A w w |  |  | Collection_1 : 1 motif | PSSM | 7.57 | 422

- 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_m3_assembly_3 | assembly_3 | cluster_3 | Collection_1 | 18 | 9.31 | 544 | +d w t G A A G A A G A r G A r r a | T Y Y T C Y T C T T C T T C A W H+ |  |
Collection_1_m10_assembly_10 | assembly_10 | cluster_2 | Collection_1 | 15 | 8.47 | 944 | r a g A s A G A G A G A s a r | Y T S T C T C T C T S T C T Y |  |
Collection_1_m4_assembly_4 | assembly_4 | cluster_3 | Collection_1 | 18 | 7.72 | 2191 | +w w T c A A G A A G A A a w+++ | +++W T T T C T T C T T G A W W+ |  |
Collection_1_m18_assembly_18 | assembly_18 | cluster_9 | Collection_1 | 11 | 6.29 | 2159 | w w T C T G A G A w w | W W T C T C A G A W W |  |
Collection_1_m1_assembly_1 | assembly_1 | cluster_2 | Collection_1 | 15 | 7.92 | 497 | +w d G c A G A G A G A c w w | W W G T C T C T C T G C H W+ |  |
Collection_1_m20_assembly_20 | assembly_20 | cluster_12 | Collection_1 | 11 | 6.36 | 2293 | w w T C A A G A C w w | W W G T C T T G A W W |  |
Collection_1_m9_assembly_9 | assembly_9 | cluster_6 | Collection_1 | 17 | 8.94 | 351 | w a A G A A A c A G c A g c A w w | W W T G C T G C T G T T T C T T W |  |
Collection_1_m12_assembly_12 | assembly_12 | cluster_1 | Collection_1 | 13 | 8.53 | 620 | ++W W G A A T C T T W+ | +w a A G A T T C w w++ |  |
Collection_1_m6_assembly_6 | assembly_6 | cluster_6 | Collection_1 | 17 | 7.18 | 394 | +++d a A G C A G C A G m w++ | ++W K C T G C T G C T T H+++ |  |
Collection_1_m2_assembly_2 | assembly_2 | cluster_3 | Collection_1 | 18 | 8.88 | 319 | T W T G A K C T T C T T C T C W W+ | +w w G A G A A G A A G m T c A w a |  |
Collection_1_m14_assembly_14 | assembly_14 | cluster_4 | Collection_1 | 10 | 8.76 | 951 | w a A G A A A G w w | W W C T T T C T T W |  |
Collection_1_m5_assembly_5 | assembly_5 | cluster_11 | Collection_1 | 11 | 6.25 | 412 | h d C C G G C G A w w | W W T C G C C G G H D |  |
Collection_1_m13_assembly_13 | assembly_13 | cluster_1 | Collection_1 | 13 | 8.36 | 152 | W W G G A G C T T C C W W | w w G G A A G C T c c w w |  |
Collection_1_m17_assembly_17 | assembly_17 | cluster_7 | Collection_1 | 10 | 8.62 | 263 | w a A G G A C A w d | H W T G T C C T T W |  |
Collection_1_m15_assembly_15 | assembly_15 | cluster_2 | Collection_1 | 15 | 6.56 | 2682 | ++++T T T T C T G T C W W | w w G A C A G A A a a++++ |  |
Collection_1_m19_assembly_19 | assembly_19 | cluster_10 | Collection_1 | 10 | 8.62 | 326 | w t C T G C A A w w | W W T T G C A G A W |  |
Collection_1_m7_assembly_7 | assembly_7 | cluster_1 | Collection_1 | 13 | 8.95 | 105 | w w T G A G C T T C C w w | W W G G A A G C T C A W W |  |
Collection_1_m16_assembly_16 | assembly_16 | cluster_5 | Collection_1 | 10 | 8.61 | 1043 | w w C A A A A G w w | W W C T T T T G W W |  |
Collection_1_m11_assembly_11 | assembly_11 | cluster_13 | Collection_1 | 12 | 7.57 | 422 | w w T G A G C T G A w w | W W T C A G C T C A W W |  |
Collection_1_m8_assembly_8 | assembly_8 | cluster_8 | Collection_1 | 11 | 6.45 | 3312 | w a A C C A C A A w w | W W T T G T G G T T W |  |
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 ## Heatmap View Distance table | PDF

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