# RSAT - matrix-clustering result

### Analysis: jan15 (15/01/2025 12:37)

## 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
4 | 1 | 4 | 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
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 | 1 | matrix-clustering_query_matrices.tab_1::4.58 | 4.58 : 1 motif | Show matrix
|  | cluster_2 | 1 | matrix-clustering_query_matrices.tab_3::4.58 | 4.58 : 1 motif | Show matrix
|  | cluster_3 | 1 | matrix-clustering_query_matrices.tab_2::4.58 | 4.58 : 1 motif | Show matrix
|  | cluster_4 | 1 | matrix-clustering_query_matrices.tab_4::4.58 | 4.58 : 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
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T T A G C W C C C k C G A T T k T G K C A r A T a G T G C g G T k G C k s T T K |  |  | 4.58 : 1 motif | PSSM | 38.11 | 999

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G y T T y G w C G K C T A T C c T A G A T T T T w C T T k G G T k s T T G |  |  | 4.58 : 1 motif | PSSM | 36.49 | 1000

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T T T G y K C m G G a G G y T w C A k C A G C A A T T w T C T G G m T k m T k s T T G |  |  | 4.58 : 1 motif | PSSM | 43.19 | 1000

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T A G G y T G C G G y T G G G C C A A C y G T T w T w T A W G T k s T k G y T G |  |  | 4.58 : 1 motif | PSSM | 39.75 | 1000

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
4.58_m4_matrix-clustering_query_matrices.tab_4 | matrix-clustering_query_matrices.tab_4 | cluster_4 | 4.58 | 40 | 39.75 | 1000 | T A G G y T G C G G y T G G G C C A A C y G T T w T w T A W G T k s T k G y T G | C A R C M A S M A C W T A W A W A A C R G T T G G C C C A R C C G C A R C C T A |  |
4.58_m1_matrix-clustering_query_matrices.tab_1 | matrix-clustering_query_matrices.tab_1 | cluster_1 | 4.58 | 40 | 38.11 | 999 | T T A G C W C C C k C G A T T k T G K C A r A T a G T G C g G T k G C k s T T K | M A A S M G C M A C C G C A C T A T Y T G M C A M A A T C G M G G G W G C T A A |  |
4.58_m3_matrix-clustering_query_matrices.tab_3 | matrix-clustering_query_matrices.tab_3 | cluster_2 | 4.58 | 37 | 36.49 | 1000 | G y T T y G w C G K C T A T C c T A G A T T T T w C T T k G G T k s T T G | C A A S M A C C M A A G W A A A A T C T A G G A T A G M C G W C R A A R C |  |
4.58_m2_matrix-clustering_query_matrices.tab_2 | matrix-clustering_query_matrices.tab_2 | cluster_3 | 4.58 | 43 | 43.19 | 1000 | T T T G y K C m G G a G G y T w C A k C A G C A A T T w T C T G G m T k m T k s T T G | C A A S M A K M A K C C A G A W A A T T G C T G M T G W A R C C T C C K G M R C A A 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