# RSAT - matrix-clustering result

### Analysis: tcp4_4 (17/09/2025 11:41)

## 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 | 3 | assembly_17::4:: assembly_15::4:: assembly_1::4:: | 4::3_motifs | Show matrix
|  | cluster_2 | 4 | assembly_3::4:: assembly_2::4:: assembly_10::4:: assembly_7::4:: | 4::4_motifs | Show matrix
|  | cluster_3 | 2 | assembly_14::4:: assembly_20::4:: | 4::2_motifs | Show matrix
|  | cluster_4 | 2 | assembly_4::4:: assembly_5::4:: | 4::2_motifs | Show matrix
|  | cluster_5 | 1 | assembly_13::4 | 4 : 1 motif | Show matrix
|  | cluster_6 | 1 | assembly_6::4 | 4 : 1 motif | Show matrix
|  | cluster_7 | 1 | assembly_9::4 | 4 : 1 motif | Show matrix
|  | cluster_8 | 2 | assembly_16::4:: assembly_19::4:: | 4::2_motifs | Show matrix
|  | cluster_9 | 1 | assembly_12::4 | 4 : 1 motif | Show matrix
|  | cluster_10 | 1 | assembly_11::4 | 4 : 1 motif | Show matrix
|  | cluster_11 | 1 | assembly_8::4 | 4 : 1 motif | Show matrix
|  | cluster_12 | 1 | assembly_18::4 | 4 : 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 | h w C C G G C G r w d |  |  | 4::2_motifs | PSSM | 5.80 | 1547
Node 2 | h w C C G G C G r w d |  |  | 4::3_motifs | PSSM | 5.75 | 1750

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | t t t y T C T T C T T C y t t T t t |  |  | 4::2_motifs | PSSM | 9.49 | 3301
Node 2 | t t t y T C T T C T T c k w t t t t |  |  | 4::3_motifs | PSSM | 8.59 | 5131
Node 3 | t t t y T C T T C T T c t w t t t t |  |  | 4::4_motifs | PSSM | 7.84 | 6273

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w C A T C T C C w w |  |  | 4::2_motifs | PSSM | 6.10 | 3872

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w w G G w T T C t w w |  |  | 4::2_motifs | PSSM | 5.60 | 8488

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C T G T G A w w |  |  | 4 : 1 motif | PSSM | 8.51 | 477

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | a a A C A G A G a w |  |  | 4 : 1 motif | PSSM | 8.80 | 744

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | d w G G A G G A d r |  |  | 4 : 1 motif | PSSM | 8.58 | 542

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | a w c C G A G y C w w |  |  | 4::2_motifs | PSSM | 7.16 | 451

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w a G A G C A C w w |  |  | 4 : 1 motif | PSSM | 8.56 | 269

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w A C A C G T C w w |  |  | 4 : 1 motif | PSSM | 6.30 | 2517

cluster_11

## 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 |  |  | 4 : 1 motif | PSSM | 8.59 | 2105

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w w C C T G G A A w w |  |  | 4 : 1 motif | PSSM | 6.25 | 2284

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
4_m5_assembly_5 | assembly_5 | cluster_4 | 4 | 11 | 6.47 | 6072 | W W G G T T T C T T W | w a A G A A A C C w w |  |
4_m14_assembly_14 | assembly_14 | cluster_3 | 4 | 11 | 6.31 | 3512 | w w C A T C T C C w w | W W G G A G A T G W W |  |
4_m18_assembly_18 | assembly_18 | cluster_12 | 4 | 11 | 6.25 | 2284 | w w C C T G G A A w w | W W T T C C A G G W W |  |
4_m9_assembly_9 | assembly_9 | cluster_7 | 4 | 10 | 8.58 | 542 | d w G G A G G A d r | Y H T C C T C C W H |  |
4_m13_assembly_13 | assembly_13 | cluster_5 | 4 | 10 | 8.51 | 477 | w w C T G T G A w w | W W T C A C A G W W |  |
4_m17_assembly_17 | assembly_17 | cluster_1 | 4 | 11 | 8.63 | 203 | W K C T C C G G Y K+ | +m r C C G G A G m w |  |
4_m20_assembly_20 | assembly_20 | cluster_3 | 4 | 11 | 8.49 | 360 | +w w A G C T C C w w | W W G G A G C T W W+ |  |
4_m6_assembly_6 | assembly_6 | cluster_6 | 4 | 10 | 8.80 | 744 | a a A C A G A G a w | W T C T C T G T T T |  |
4_m4_assembly_4 | assembly_4 | cluster_4 | 4 | 11 | 6.31 | 2416 | w w G G A T T C C w w | W W G G A A T C C W W |  |
4_m7_assembly_7 | assembly_7 | cluster_2 | 4 | 18 | 8.89 | 1559 | t t t y T C T T C T T C k t y+++ | +++R A M G A A G A A G A R A A A |  |
4_m15_assembly_15 | assembly_15 | cluster_1 | 4 | 11 | 6.18 | 645 | H W C C G G C G G H D | h d C C G C C G G w d |  |
4_m3_assembly_3 | assembly_3 | cluster_2 | 4 | 18 | 8.29 | 1142 | +W W M R A G A A G A A G C T W W+ | +w w A g C T T C T T C T y k w w+ |  |
4_m1_assembly_1 | assembly_1 | cluster_1 | 4 | 11 | 6.21 | 902 | h w C C G G C G A w d | H W T C G C C G G W D |  |
4_m12_assembly_12 | assembly_12 | cluster_9 | 4 | 10 | 8.56 | 269 | w a G A G C A C w w | W W G T G C T C T W |  |
4_m10_assembly_10 | assembly_10 | cluster_2 | 4 | 18 | 9.98 | 1742 | T T T Y T C T T C T T C Y T T T T T | a a A A A r G A A G A A G A r a a a |  |
4_m16_assembly_16 | assembly_16 | cluster_8 | 4 | 11 | 8.48 | 158 | a w C C G A G C h a+ | +T D G C T C G G W T |  |
4_m19_assembly_19 | assembly_19 | cluster_8 | 4 | 11 | 8.50 | 293 | +w w C G A G T C w w | W W G A C T C G W W+ |  |
4_m8_assembly_8 | assembly_8 | cluster_11 | 4 | 10 | 8.59 | 2105 | w w C A A A A G w w | W W C T T T T G W W |  |
4_m11_assembly_11 | assembly_11 | cluster_10 | 4 | 11 | 6.30 | 2517 | w w A C A C G T C w w | W W G A C G T G T W W |  |
4_m2_assembly_2 | assembly_2 | cluster_2 | 4 | 18 | 8.75 | 1830 | +T Y T T C T T C T T G K W W W++ | ++w w w m c A A G A A G A A r a+ |  |
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