# RSAT - matrix-clustering result

### Analysis: citt (01/07/2026 09:52)

## 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
8 | 1 | 3 | Download | Download |
average | Ncor | Ncor = 0.4 cor = 0.4

| Logo Forest (dynamic browsing) Logo Forest (rapid overview - low image quality) cluster_1 cluster_2 cluster_3
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 | errorGettingCRtag_CitB::Collection_1:: AEASRTTRR_CitT::Collection_1:: AEIARVTRR_DctR::Collection_1:: | Collection_1::3_motifs | Show matrix
|  | cluster_2 | 2 | TEISQVSRK_MaeM::Collection_1:: TDISRVSRK_DcuR::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_3 | 3 | TEISQVSRK_MalR::Collection_1:: ADSSKTTRR_CitB::Collection_1:: AEISRTTRR_CitB::Collection_1:: | Collection_1::3_motifs | 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
Display Logo Trees
cluster_1
cluster_2
cluster_3
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w G A m C A A A A w G A M C A A A A--- |  |  | Collection_1::2_motifs | PSSM | 16.15 | 40
Node 2 | w G A m C w W A A T G A A C A A A A k T C |  |  | Collection_1::3_motifs | PSSM | 17.02 | 50

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | r t t T T W T k w A A y T A A A A W A A k |  |  | Collection_1::2_motifs | PSSM | 15.18 | 47

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | t w A A T W A A A w y m A T T A A A w m a m T w A A A a m m m- |  |  | Collection_1::2_motifs | PSSM | 17.84 | 64
Node 2 | t w w a T T A A A w y m A T w A A A w a a m T w A W A a m y w w |  |  | Collection_1::3_motifs | PSSM | 15.50 | 82

- 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_m7_errorGettingCRtag_CitB | errorGettingCRtag_CitB | cluster_1 | Collection_1 | 21 | 16.45 | 10 | +G A M Y T W W R T G C A Y W W A R K T C | G A m y T w w r T G C A y w w A r k T C+ |  |
Collection_1_m1_AEASRTTRR_CitT | AEASRTTRR_CitT | cluster_1 | Collection_1 | 21 | 18.51 | 22 | T G A A C w w w A T G A A C A W A A+++ | +++T T W T G T T C A T W W W G T T C A |  |
Collection_1_m6_TDISRVSRK_DcuR | TDISRVSRK_DcuR | cluster_2 | Collection_1 | 21 | 16.34 | 29 | +++T T T T G T A A Y T A A A R W A A+ | +T T w y T T T A r T T A C A A A A+++ |  |
Collection_1_m2_AEIARVTRR_DctR | AEIARVTRR_DctR | cluster_1 | Collection_1 | 21 | 18.94 | 18 | a k A C C A A A A w G A m C A A A A+++ | +++T T T T G K T C W T T T T G G T M T |  |
Collection_1_m3_TEISQVSRK_MaeM | TEISQVSRK_MaeM | cluster_2 | Collection_1 | 21 | 15.48 | 18 | r t t T T w T T a A w w T A A A A A A m k | M K T T T T T T A W W T T A A W A A A A Y |  |
Collection_1_m8_TEISQVSRK_MalR | TEISQVSRK_MalR | cluster_3 | Collection_1 | 32 | 17.61 | 18 | +W W A T T W A A W W W W W W W W W W W W W W W T T W A A T W W | w w a t T w A A w w w w w w w w w w w w w w w T T w A a t w w+ |  |
Collection_1_m5_AEISRTTRR_CitB | AEISRTTRR_CitB | cluster_3 | Collection_1 | 32 | 18.27 | 47 | ++++t T A A A w y m A T T A A A w m A m T w A A A a m m m+ | +K K K T T T T W A K T K W T T T A A T K R W T T T A A++++ |  |
Collection_1_m4_ADSSKTTRR_CitB | ADSSKTTRR_CitB | cluster_3 | Collection_1 | 32 | 18.22 | 17 | t w A A T A A A m a c C A T w A A a t t m A T A A A r a m+++ | +++K T Y T T T A T K A A T T T W A T G G T K T T T A T T W 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