# RSAT - matrix-clustering result

### Analysis: argr (18/06/2026 09:35)

## 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
14 | 1 | 4 | Download | Download |
average | Ncor | Ncor = 0.55 cor = 0.6

| Logo Forest (dynamic browsing) Logo Forest (rapid overview - low image quality) cluster_1 cluster_2 cluster_3 cluster_4
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 | 11 | TQATSR_ArgR::Collection_1:: SQAKSR_ArgR::Collection_1:: SQSKNR_ArgR::Collection_1:: TQSSSR_ArgR::Collection_1:: TQSTSR_ArgR::Collection_1:: TQATSR_ArgR_18bp::Collection_1:: TQTTSR_ArgR::Collection_1:: SQSKSR_ArgR::Collection_1:: SQPQSR_ArgR::Collection_1:: AQATSR_ArgR::Collection_1:: SQGTSR_ArgR::Collection_1:: | Collection_1::11_motifs | Show matrix
|  | cluster_2 | 1 | TQGTSR_ArgR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_3 | 1 | VQPTAR_ArgR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_4 | 1 | NQSKSR_ArgR::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
Display Logo Trees
cluster_1
cluster_2
cluster_3
cluster_4
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | ---w t T G m A T A w w T A T k C A a w--- |  |  | Collection_1::2_motifs | PSSM | 11.16 | 120
Node 2 | ---w w T G w A T A w w T A T w C A w w--- |  |  | Collection_1::2_motifs | PSSM | 10.79 | 346
Node 3 | ---w t T G m A T A w w T A T k C A a w--- |  |  | Collection_1::3_motifs | PSSM | 11.13 | 128
Node 4 | ---w w T G w A T A w w T A T w C A w w--- |  |  | Collection_1::5_motifs | PSSM | 10.43 | 474
Node 5 | ---w k T r A A T A w w T A T T y A m w--- |  |  | Collection_1::2_motifs | PSSM | 13.80 | 26
Node 6 | ---w w T G w A T A w w T A T w C A w w--- |  |  | Collection_1::6_motifs | PSSM | 10.40 | 486
Node 7 | ---w w T G w A T A w w T A T w C A w w--- |  |  | Collection_1::8_motifs | PSSM | 10.40 | 512
Node 8 | ----S T G a A T A w w T A T t C A S---- |  |  | Collection_1::2_motifs | PSSM | 13.55 | 34
Node 9 | ---w w T G w A T A w w T A T w C A w w--- |  |  | Collection_1::10_motifs | PSSM | 10.39 | 546
Node 10 | w w w w w T G w A T A w w T A T w C A w w w w w |  |  | Collection_1::11_motifs | PSSM | 11.96 | 568

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y k h A d r n y h T d m r |  |  | Collection_1 : 1 motif | PSSM | 9.10 | 4

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | W T m W W K A T r s y A T M W W k A W |  |  | Collection_1 : 1 motif | PSSM | 17.48 | 20

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w r T G m A T w w w w A T k C A w w w w w w w T G m w T w w w w a T k m w y w w |  |  | Collection_1 : 1 motif | PSSM | 20.83 | 23

- 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_m4_AQATSR_ArgR | AQATSR_ArgR | cluster_1 | Collection_1 | 24 | 12.14 | 30 | +++++T G A A T A w w T A T T C A+++++ | +++++T G A A T A W W T A T T C A+++++ |  |
Collection_1_m12_TQGTSR_ArgR | TQGTSR_ArgR | cluster_2 | Collection_1 | 13 | 9.10 | 4 | Y K h A d R n Y h T d M R | Y K H A D R N Y H T D M R |  |
Collection_1_m7_VQPTAR_ArgR | VQPTAR_ArgR | cluster_3 | Collection_1 | 19 | 17.48 | 20 | W T M W W K A T r s y A T M W W K A W | W T M W W K A T R S Y A T M W W K A W |  |
Collection_1_m1_NQSKSR_ArgR | NQSKSR_ArgR | cluster_4 | Collection_1 | 40 | 20.83 | 23 | w r T G m A T w W w w A T k C A w w w w w w w T G m w T w w w w A T k m w y w w | W W R W K M A T W W W W A W K C A W W W W W W W T G M A T W W W W A T K C A Y W |  |
Collection_1_m13_TQSTSR_ArgR | TQSTSR_ArgR | cluster_1 | Collection_1 | 24 | 13.46 | 30 | +++w w T g T A T W w w W A T A c A w w+++ | +++W W T G T A T W W W W A T A C A W W+++ |  |
Collection_1_m9_TQATSR_ArgR_18bp | TQATSR_ArgR_18bp | cluster_1 | Collection_1 | 24 | 10.69 | 316 | +++w w T G w A T A w w T A T w C A w w+++ | +++W W T G W A T A W W T A T W C A W W+++ |  |
Collection_1_m11_SQAKSR_ArgR | SQAKSR_ArgR | cluster_1 | Collection_1 | 24 | 13.99 | 14 | +++A t T r A r T A w w T A y T y A a T+++ | +++A T T R A R T A W W T A Y T Y A A T+++ |  |
Collection_1_m6_TQSSSR_ArgR | TQSSSR_ArgR | cluster_1 | Collection_1 | 24 | 12.88 | 12 | +++A W W R M A T A W W T A T K Y W W T+++ | +++a w w r M A T A w w T A T K y w w t+++ |  |
Collection_1_m14_SQSKNR_ArgR | SQSKNR_ArgR | cluster_1 | Collection_1 | 24 | 16.96 | 12 | +++w r T R A A T A w w T A T T Y A y w+++ | +++W R T R A A T A W W T A T T Y A Y W+++ |  |
Collection_1_m2_TQATSR_ArgR | TQATSR_ArgR | cluster_1 | Collection_1 | 24 | 15.62 | 22 | W W W M W T K W A T W W W W A T W M A W K W W W | w w w m w T k w A T w w w w A T w m A w k w w w |  |
Collection_1_m8_SQGTSR_ArgR | SQGTSR_ArgR | cluster_1 | Collection_1 | 24 | 17.68 | 4 | ++++S Y G Y A T A W W T A T R C R S++++ | ++++S Y G Y A T A W W T A T R C R S++++ |  |
Collection_1_m3_SQPQSR_ArgR | SQPQSR_ArgR | cluster_1 | Collection_1 | 24 | 13.34 | 18 | +++w t T R m A T A w w T A T k Y A a w+++ | +++W T T R M A T A W W T A T K Y A A W+++ |  |
Collection_1_m5_TQTTSR_ArgR | TQTTSR_ArgR | cluster_1 | Collection_1 | 24 | 14.51 | 8 | +++W T W G M A T W W W W A T K C W A W+++ | +++w T W G m A T W w w W A T k C W A w+++ |  |
Collection_1_m10_SQSKSR_ArgR | SQSKSR_ArgR | cluster_1 | Collection_1 | 24 | 11.06 | 102 | +++w t T G m A T A w w T A T k C A a w+++ | +++W T T G M A T A W W T A T K C A A 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