# RSAT - matrix-clustering result

### Analysis: tcp4_3 (17/09/2025 10:25)

## 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
16 | 1 | 11 | 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
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 | 4 | assembly_2::3:: assembly_15::3:: assembly_1::3:: assembly_8::3:: | 3::4_motifs | Show matrix
|  | cluster_2 | 2 | assembly_13::3:: assembly_5::3:: | 3::2_motifs | Show matrix
|  | cluster_3 | 2 | assembly_11::3:: assembly_16::3:: | 3::2_motifs | Show matrix
|  | cluster_4 | 1 | assembly_3::3 | 3 : 1 motif | Show matrix
|  | cluster_5 | 1 | assembly_9::3 | 3 : 1 motif | Show matrix
|  | cluster_6 | 1 | assembly_4::3 | 3 : 1 motif | Show matrix
|  | cluster_7 | 1 | assembly_6::3 | 3 : 1 motif | Show matrix
|  | cluster_8 | 1 | assembly_14::3 | 3 : 1 motif | Show matrix
|  | cluster_9 | 1 | assembly_10::3 | 3 : 1 motif | Show matrix
|  | cluster_10 | 1 | assembly_12::3 | 3 : 1 motif | Show matrix
|  | cluster_11 | 1 | assembly_7::3 | 3 : 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
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | t t y y T C T T C T T C k t y- |  |  | 3::2_motifs | PSSM | 8.54 | 1518
Node 2 | t t y y T C T T C T T C k y y t |  |  | 3::3_motifs | PSSM | 8.66 | 2135
Node 3 | t t y y T C T T C T T C t y y t |  |  | 3::4_motifs | PSSM | 7.98 | 2782

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w G A G C A A s a w w |  |  | 3::2_motifs | PSSM | 6.30 | 1420

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w g A C A m A G w w |  |  | 3::2_motifs | PSSM | 6.40 | 1395

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C T T C A C w w |  |  | 3 : 1 motif | PSSM | 8.49 | 285

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C A A C A C w w |  |  | 3 : 1 motif | PSSM | 8.72 | 288

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w A C A G T T T C w w |  |  | 3 : 1 motif | PSSM | 7.83 | 601

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w G A A G C T C C w w |  |  | 3 : 1 motif | PSSM | 7.61 | 227

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | m w C G T G A C w w |  |  | 3 : 1 motif | PSSM | 8.55 | 109

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y a G C C G C A G A w r |  |  | 3 : 1 motif | PSSM | 7.74 | 97

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a A C G A C C a w |  |  | 3 : 1 motif | PSSM | 8.58 | 98

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | a w A G A G C C w w |  |  | 3 : 1 motif | PSSM | 8.54 | 127

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3_m8_assembly_8 | assembly_8 | cluster_1 | 3 | 16 | 8.97 | 786 | t t c k T C T T C T T C k t y+ | +R A M G A A G A A G A M G A A |  |
3_m12_assembly_12 | assembly_12 | cluster_10 | 3 | 10 | 8.58 | 98 | w a A C G A C C a w | W T G G T C G T T W |  |
3_m9_assembly_9 | assembly_9 | cluster_5 | 3 | 10 | 8.72 | 288 | w w C A A C A C w w | W W G T G T T G W W |  |
3_m4_assembly_4 | assembly_4 | cluster_6 | 3 | 12 | 7.83 | 601 | w w A C A G T T T C w w | W W G A A A C T G T W W |  |
3_m15_assembly_15 | assembly_15 | cluster_1 | 3 | 16 | 9.27 | 617 | +T Y Y T C T T C T T C T Y Y T | a r r A G A A G A A G A r r a+ |  |
3_m3_assembly_3 | assembly_3 | cluster_4 | 3 | 10 | 8.49 | 285 | w w C T T C A C w w | W W G T G A A G W W |  |
3_m6_assembly_6 | assembly_6 | cluster_7 | 3 | 12 | 7.61 | 227 | w w G A A G C T C C w w | W W G G A G C T T C W W |  |
3_m1_assembly_1 | assembly_1 | cluster_1 | 3 | 16 | 8.38 | 732 | +t y y T C T T C T T C k t y+ | +R A M G A A G A A G A R R A+ |  |
3_m5_assembly_5 | assembly_5 | cluster_2 | 3 | 12 | 7.69 | 473 | w w G A G C A A G A a w | W T T C T T G C T C W W |  |
3_m10_assembly_10 | assembly_10 | cluster_9 | 3 | 12 | 7.74 | 97 | y a G C C G C A G A w r | Y W T C T G C G G C T R |  |
3_m16_assembly_16 | assembly_16 | cluster_3 | 3 | 11 | 6.37 | 835 | w w G A C A C A G w w | W W C T G T G T C W W |  |
3_m14_assembly_14 | assembly_14 | cluster_8 | 3 | 10 | 8.55 | 109 | m w C G T G A C w w | W W G T C A C G W K |  |
3_m7_assembly_7 | assembly_7 | cluster_11 | 3 | 10 | 8.54 | 127 | a w A G A G C C w w | W W G G C T C T W T |  |
3_m11_assembly_11 | assembly_11 | cluster_3 | 3 | 11 | 8.60 | 560 | +a a A C A A A G w w | W W C T T T G T T T+ |  |
3_m13_assembly_13 | assembly_13 | cluster_2 | 3 | 12 | 6.42 | 947 | w w G A G C A A C w w+ | +W W G T T G C T C W W |  |
3_m2_assembly_2 | assembly_2 | cluster_1 | 3 | 16 | 7.76 | 647 | +W R G A G A A G A G W W+++ | +++w w C T C T T C T C y 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