# RSAT - matrix-clustering result

### Analysis: f (09/01/2026 16:29)

## 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 | 6 | 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
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 | 10 | assembly_3::f:: assembly_6::f:: assembly_7::f:: assembly_15::f:: assembly_12::f:: assembly_2::f:: assembly_10::f:: assembly_9::f:: assembly_18::f:: assembly_4::f:: | f::10_motifs | Show matrix
|  | cluster_2 | 5 | assembly_8::f:: assembly_14::f:: assembly_16::f:: assembly_17::f:: assembly_5::f:: | f::5_motifs | Show matrix
|  | cluster_3 | 2 | assembly_1::f:: assembly_20::f:: | f::2_motifs | Show matrix
|  | cluster_4 | 1 | assembly_11::f | f : 1 motif | Show matrix
|  | cluster_5 | 1 | assembly_19::f | f : 1 motif | Show matrix
|  | cluster_6 | 1 | assembly_13::f | f : 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
Display Logo Trees
cluster_1
cluster_2
cluster_3
cluster_4
cluster_5
cluster_6
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | ------wwwtwTTATATAATkTww |  |  | f::2_motifs | PSSM | 8.62 | 5760
Node 2 | ------wwwtwTTATATAATkTww |  |  | f::3_motifs | PSSM | 8.42 | 6731
Node 3 | ------wwwwtwTATATAATkTww |  |  | f::4_motifs | PSSM | 8.16 | 8259
Node 4 | ------------wwarTAATGTww |  |  | f::2_motifs | PSSM | 6.50 | 7374
Node 5 | ----------wwaawrTAATgTww |  |  | f::3_motifs | PSSM | 6.70 | 12268
Node 6 | ----wwwwwwtwTATATAATkTww |  |  | f::5_motifs | PSSM | 8.09 | 9432
Node 7 | wwahwwwwwwtwTATATAATkTww |  |  | f::6_motifs | PSSM | 9.04 | 10022
Node 8 | ----------wwaawrTAATGTww |  |  | f::4_motifs | PSSM | 6.67 | 14102
Node 9 | wwahwwwwwwwwwAwATAATgTww |  |  | f::10_motifs | PSSM | 8.26 | 24124

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | wwAATAAwAww- |  |  | f::2_motifs | PSSM | 6.38 | 40330
Node 2 | aaAAAAArAaww |  |  | f::2_motifs | PSSM | 7.04 | 25376
Node 3 | waAAwAAaAwww |  |  | f::4_motifs | PSSM | 6.12 | 65706
Node 4 | waAAwAAaAwww |  |  | f::5_motifs | PSSM | 5.80 | 74121

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | wwTATAGwATww |  |  | f::2_motifs | PSSM | 7.26 | 3939

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | waAACGTGww |  |  | f : 1 motif | PSSM | 8.66 | 350

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | wwATACGTATww |  |  | f : 1 motif | PSSM | 7.87 | 1476

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | wwCAACTAww |  |  | f : 1 motif | PSSM | 8.68 | 751

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
f_m20_assembly_20 | assembly_20 | cluster_3 | f | 12 | 8.83 | 1194 | wwTATAGAww++ | ++WWTCTATAWW |  |
f_m4_assembly_4 | assembly_4 | cluster_1 | f | 24 | 7.77 | 3302 | ++++++++++++wwAATAATGTww | WWACATTATTWW++++++++++++ |  |
f_m9_assembly_9 | assembly_9 | cluster_1 | f | 24 | 7.71 | 4894 | ++++++++++WWACATTATATTWW | wwAATATAATgTww++++++++++ |  |
f_m19_assembly_19 | assembly_19 | cluster_5 | f | 12 | 7.87 | 1476 | wwATACGTATww | WWATACGTATWW |  |
f_m17_assembly_17 | assembly_17 | cluster_2 | f | 12 | 7.14 | 19355 | aaAAAAArAaw+ | +WTTYTTTTTTT |  |
f_m15_assembly_15 | assembly_15 | cluster_1 | f | 24 | 9.26 | 971 | ++++++WWWGTGTATATAATGTWW | wwAcATTATATAcAcwww++++++ |  |
f_m10_assembly_10 | assembly_10 | cluster_1 | f | 24 | 8.68 | 1834 | ++++++++++++++WWACATTTTW | waAAATGTww++++++++++++++ |  |
f_m16_assembly_16 | assembly_16 | cluster_2 | f | 12 | 6.91 | 24934 | waAAwAAAAww+ | +WWTTTTWTTTW |  |
f_m18_assembly_18 | assembly_18 | cluster_1 | f | 24 | 6.50 | 4072 | +++++++++++++WWGTAATGTWW | wwACATTACww+++++++++++++ |  |
f_m13_assembly_13 | assembly_13 | cluster_6 | f | 10 | 8.68 | 751 | wwCAACTAww | WWTAGTTGWW |  |
f_m12_assembly_12 | assembly_12 | cluster_1 | f | 24 | 8.66 | 4132 | +++++++WWTTTTATATAATKTWW | wwAmATTATATAAAaww+++++++ |  |
f_m1_assembly_1 | assembly_1 | cluster_3 | f | 12 | 7.92 | 2745 | wwTATAGTATww | WWATACTATAWW |  |
f_m14_assembly_14 | assembly_14 | cluster_2 | f | 12 | 6.62 | 15396 | wwAATAATAww+ | +WWTATTATTWW |  |
f_m8_assembly_8 | assembly_8 | cluster_2 | f | 12 | 6.70 | 8415 | WWTTTTGTCWW+ | +wwgACAAAAww |  |
f_m2_assembly_2 | assembly_2 | cluster_1 | f | 24 | 9.47 | 1628 | ++++++WWAHATTATATAATDTWW | wwAhATTATATAATdTww++++++ |  |
f_m7_assembly_7 | assembly_7 | cluster_1 | f | 24 | 9.67 | 1528 | ++++++wwAATAyATATAATkwww | WWWMATTATATRTATTWW++++++ |  |
f_m5_assembly_5 | assembly_5 | cluster_2 | f | 12 | 7.54 | 6021 | waAAAAAGtAww | WWTACTTTTTTW |  |
f_m3_assembly_3 | assembly_3 | cluster_1 | f | 24 | 12.11 | 590 | WWAHATTATATRTATATAATDTWW | wwahATTATATAyATATAATdtww |  |
f_m11_assembly_11 | assembly_11 | cluster_4 | f | 10 | 8.66 | 350 | waAACGTGww | WWCACGTTTW |  |
f_m6_assembly_6 | assembly_6 | cluster_1 | f | 24 | 9.52 | 1173 | ++++WWWTTTCACATATAATKTWW | wwAmATTATATgTgAAAwww++++ |  |
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