# RSAT - matrix-clustering result

### Analysis: citb (11/08/2026 09:23)

## 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 | 1 | Download | Download |
average | Ncor | Ncor = 0.3 cor = 0.4

| Logo Forest (dynamic browsing) Logo Forest (rapid overview - low image quality) cluster_1
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 | 16 | ATVSRATQR_CitB::Collection_1:: IEASRTTRR_CitT::Collection_1:: AEIARVTRR_DctRRegPrecise::Collection_1:: IEVSRTTRR_CitT::Collection_1:: AEIARVTRR_DctR::Collection_1:: ADVSRTTRR_CitT::Collection_1:: AEASRTTRR_CitT::Collection_1:: AEASRTTRR_CitTRegPrecise::Collection_1:: AMASRSTRR_CitT::Collection_1:: AEVSRSTRR_CitT::Collection_1:: ASISRSTRR_CitT::Collection_1:: TEISQVSRK_MaeM::Collection_1:: TDISRVSRK_DcuR::Collection_1:: TEISQVSRK_MalR::Collection_1:: ADSSKTTRR_CitB::Collection_1:: AEISRTTRR_CitB::Collection_1:: | Collection_1::16_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

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cluster_1
Display Logo Trees
cluster_1
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -----T G A A C A A A A T G A A C A A A A---------- |  |  | Collection_1::2_motifs | PSSM | 24.95 | 2
Node 2 | -----T G A A C A A A A T G A A C A A A A---------- |  |  | Collection_1::3_motifs | PSSM | 23.45 | 8
Node 3 | -----T G A A C A A A A T G A A C A A A A---------- |  |  | Collection_1::4_motifs | PSSM | 21.92 | 14
Node 4 | -----T G A A C W W W A T G A A C A A A A---------- |  |  | Collection_1::5_motifs | PSSM | 18.83 | 36
Node 5 | -----T G A A C A A A A T G A A C A A A A---------- |  |  | Collection_1::6_motifs | PSSM | 18.87 | 37
Node 6 | -----T G A m C A A A A W G A A C A A A A---------- |  |  | Collection_1::7_motifs | PSSM | 16.96 | 55
Node 7 | --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
Node 8 | -----T G A A C A A A A w G A A C A W A A---------- |  |  | Collection_1::8_motifs | PSSM | 16.47 | 65
Node 9 | 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 10 | -----W G A m C A A A A w G A M C A A A A y G T C C----- |  |  | Collection_1::9_motifs | PSSM | 21.32 | 73
Node 11 | -----W G A m C A A A A w G A m C A A A A y G T C C----- |  |  | Collection_1::10_motifs | PSSM | 20.22 | 79
Node 12 | -----W G A m C A A A A w G A a C A A A A y k y C C----- |  |  | Collection_1::11_motifs | PSSM | 18.09 | 83
Node 13 | t w A A 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 a w w |  |  | Collection_1::3_motifs | PSSM | 17.54 | 72
Node 14 | t w a w t T w w w w t a A T T A A A w a A m T w A A A a m m a w w |  |  | Collection_1::5_motifs | PSSM | 16.29 | 119
Node 15 | t w a w t T d A a y w A A w t r A A m a A A w w A A A m m m a w w |  |  | Collection_1::16_motifs | PSSM | 14.10 | 202

- 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_m5_AEISRTTRR_CitB | AEISRTTRR_CitB | cluster_1 | Collection_1 | 33 | 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_m6_TDISRVSRK_DcuR | TDISRVSRK_DcuR | cluster_1 | Collection_1 | 33 | 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_m13_ATVSRATQR_CitB | ATVSRATQR_CitB | cluster_1 | Collection_1 | 33 | 16.73 | 4 | ++++++G A S Y W Y W R K R C A H H M W R N K C+++++++ | +++++++G M n y W K d d T G Y M y w R w r s T C++++++ |  |
Collection_1_m3_TEISQVSRK_MaeM | TEISQVSRK_MaeM | cluster_1 | Collection_1 | 33 | 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_m2_AEIARVTRR_DctR | AEIARVTRR_DctR | cluster_1 | Collection_1 | 33 | 18.94 | 18 | +++++T T T T G K T C W T T T T G G T M T++++++++++ | ++++++++++a k A C C A A A A w G A m C A A A A+++++ |  |
Collection_1_m16_TEISQVSRK_MalR | TEISQVSRK_MalR | cluster_1 | Collection_1 | 33 | 22.23 | 8 | ++W A S T W A A W W W W Y T V D T W K W Y W W W T W W A W D W W | w w h W T w w A w w w r w m W A h b A r w w W W T T W A s T w++ |  |
Collection_1_m1_AEASRTTRR_CitT | AEASRTTRR_CitT | cluster_1 | Collection_1 | 33 | 18.51 | 22 | +++++T T W T G T T C A T W W W G T T C A++++++++++ | ++++++++++T G A A C w w w A T G A A C A W A A+++++ |  |
Collection_1_m7_ADVSRTTRR_CitT | ADVSRTTRR_CitT | cluster_1 | Collection_1 | 33 | 24.95 | 1 | +++++T T T T G T T C T T T T T G T T C A++++++++++ | ++++++++++T G A A C A A A A A G A A C A A A A+++++ |  |
Collection_1_m8_AEASRTTRR_CitTRegPrecise | AEASRTTRR_CitTRegPrecise | cluster_1 | Collection_1 | 33 | 21.51 | 6 | +++++T T T T G T T Y W T T T T G W Y C A++++++++++ | ++++++++++T G r w C A A A A w r A A C A A A A+++++ |  |
Collection_1_m11_AMASRSTRR_CitT | AMASRSTRR_CitT | cluster_1 | Collection_1 | 33 | 23.15 | 6 | +++++T T T T G T T C A T T T T G T T C A++++++++++ | ++++++++++T G A A C A A A A T G A A C A A A A+++++ |  |
Collection_1_m14_IEASRTTRR_CitT | IEASRTTRR_CitT | cluster_1 | Collection_1 | 33 | 21.35 | 6 | +++++C T T T G C G T G A T T T C T T C A++++++++++ | ++++++++++T G A A G A A A T C A C G C A A A G+++++ |  |
Collection_1_m15_IEVSRTTRR_CitT | IEVSRTTRR_CitT | cluster_1 | Collection_1 | 33 | 24.95 | 10 | +++++T T A A A T C C T T T T T G T T C A++++++++++ | ++++++++++T G A A C A A A A A G G A T T T A A+++++ |  |
Collection_1_m9_AEIARVTRR_DctRRegPrecise | AEIARVTRR_DctRRegPrecise | cluster_1 | Collection_1 | 33 | 28.60 | 8 | +++++G G A C R T T T T G G T C T T T T T G G T C T+++++ | +++++A G A C C A A A A A G A C C A A A A y G T C C+++++ |  |
Collection_1_m10_AEVSRSTRR_CitT | AEVSRSTRR_CitT | cluster_1 | Collection_1 | 33 | 24.95 | 1 | +++++T G A A C A A A A T G A A C A A A A++++++++++ | ++++++++++T T T T G T T C A T T T T G T T C A+++++ |  |
Collection_1_m4_ADSSKTTRR_CitB | ADSSKTTRR_CitB | cluster_1 | Collection_1 | 33 | 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 |  |
Collection_1_m12_ASISRSTRR_CitT | ASISRSTRR_CitT | cluster_1 | Collection_1 | 33 | 24.95 | 1 | +++++T G A A C A A A A T G A A C A A A A++++++++++ | ++++++++++T T T T G T T C A T T T T G T T C 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