# RSAT - matrix-clustering result

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

## 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 | 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
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
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w T T c A A G A A G a A v a w |  |  | 2::2_motifs | PSSM | 7.84 | 1254
Node 2 | w w w k C A A G A A G A m w w- |  |  | 2::2_motifs | PSSM | 8.08 | 737
Node 3 | w w t T c A A G A A G A a a w w |  |  | 2::4_motifs | PSSM | 7.60 | 1991
Node 4 | w w T T C A A G A A m h w w w- |  |  | 2::2_motifs | PSSM | 7.13 | 1829
Node 5 | -w w w a s A G A A G A c a w- |  |  | 2::2_motifs | PSSM | 7.18 | 1004
Node 6 | w w t T C A A G A A g a a a w w |  |  | 2::6_motifs | PSSM | 7.05 | 3820
Node 7 | w w t t c A A G A A g a m a w w |  |  | 2::8_motifs | PSSM | 6.43 | 4824

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w w G C A r C A w w |  |  | 2::2_motifs | PSSM | 5.47 | 2766

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w m A C G T G G C w w |  |  | 2 : 1 motif | PSSM | 6.43 | 621

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C T T G G A w w |  |  | 2 : 1 motif | PSSM | 8.57 | 277

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w A A C A G C T w w |  |  | 2 : 1 motif | PSSM | 6.31 | 1344

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w t C T T C A C w w |  |  | 2 : 1 motif | PSSM | 8.59 | 289

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | a a a c A G A G A G A c T w w |  |  | 2 : 1 motif | PSSM | 8.45 | 354

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A T G A G A w w |  |  | 2 : 1 motif | PSSM | 8.60 | 524

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | r r C G G C G A k d |  |  | 2 : 1 motif | PSSM | 8.46 | 76

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y w T C A A C G C C w w |  |  | 2 : 1 motif | PSSM | 7.73 | 204

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A C G A A C w w |  |  | 2 : 1 motif | PSSM | 8.61 | 169

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | r w G G A G G A d d |  |  | 2 : 1 motif | PSSM | 8.69 | 201

- 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 | w w T T C A A G A A m w w+++ | +++W W K T T C T T G A A W W |  |
2_m1_assembly_1 | assembly_1 | cluster_7 | 2 | 15 | 8.45 | 354 | a a a c A G A G A G A c T w w | W W A G T C T C T C T G T T T |  |
2_m5_assembly_5 | assembly_5 | cluster_1 | 2 | 16 | 8.93 | 263 | w a A g c A A G A A G A c w a+ | +T W G T C T T C T T G C T T W |  |
2_m4_assembly_4 | assembly_4 | cluster_1 | 2 | 16 | 8.41 | 272 | D W T T C A A G A A G C T W W+ | +w w A G C T T C T T G A A w h |  |
2_m18_assembly_18 | assembly_18 | cluster_5 | 2 | 11 | 6.31 | 1344 | w w A A C A G C T w w | W W A G C T G T T W W |  |
2_m16_assembly_16 | assembly_16 | cluster_2 | 2 | 11 | 6.23 | 891 | w w T G C A G C A w w | W W T G C T G C A W W |  |
2_m10_assembly_10 | assembly_10 | cluster_2 | 2 | 11 | 6.34 | 1875 | w a A G C A A C A w w | W W T G T T G C T T W |  |
2_m17_assembly_17 | assembly_17 | cluster_11 | 2 | 10 | 8.61 | 169 | w a A C G A A C w w | W W G T T C G T T W |  |
2_m14_assembly_14 | assembly_14 | cluster_10 | 2 | 12 | 7.73 | 204 | y w T C A A C G C C w w | W W G G C G T T G A W R |  |
2_m6_assembly_6 | assembly_6 | cluster_1 | 2 | 16 | 8.10 | 459 | w w T T c A A G A A G m A r a w | W T Y T K C T T C T T G A A W W |  |
2_m19_assembly_19 | assembly_19 | cluster_1 | 2 | 16 | 8.23 | 795 | w w T T c A A G A A G A A m w w | W W K T T C T T C T T G A A W W |  |
2_m7_assembly_7 | assembly_7 | cluster_1 | 2 | 16 | 7.83 | 525 | +++W W G A G A A G A C A W+ | +w t g T C T T C T C w w+++ |  |
2_m13_assembly_13 | assembly_13 | cluster_12 | 2 | 10 | 8.69 | 201 | r w G G A G G A d d | H H T C C T C C W Y |  |
2_m15_assembly_15 | assembly_15 | cluster_3 | 2 | 11 | 6.43 | 621 | w m A C G T G G C w w | W W G C C A C G T K W |  |
2_m8_assembly_8 | assembly_8 | cluster_8 | 2 | 10 | 8.60 | 524 | w a A T G A G A w w | W W T C T C A T T W |  |
2_m11_assembly_11 | assembly_11 | cluster_9 | 2 | 10 | 8.46 | 76 | r r C G G C G A k d | H M T C G C C G Y Y |  |
2_m2_assembly_2 | assembly_2 | cluster_1 | 2 | 16 | 8.38 | 474 | w w t T C A A G A A G A m a w+ | +W T K T C T T C T T G A A W W |  |
2_m12_assembly_12 | assembly_12 | cluster_6 | 2 | 10 | 8.59 | 289 | w t C T T C A C w w | W W G T G A A G A W |  |
2_m3_assembly_3 | assembly_3 | cluster_1 | 2 | 16 | 7.45 | 479 | +w w a m C A G A A G A c w w+ | +W W G T C T T C T G K T W W+ |  |
2_m20_assembly_20 | assembly_20 | cluster_4 | 2 | 10 | 8.57 | 277 | w w C T T G G A w w | W W T C C A A G W 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