# RSAT - matrix-clustering result

### Analysis: jan06 (06/01/2025 07:22)

## 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 | 2 | 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
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 | matrix-clustering_query_matrices.tab_4::3.1039:: matrix-clustering_query_matrices.tab_2::3.1039:: matrix-clustering_query_matrices.tab_3::3.1039:: | 3.1039::3_motifs | Show matrix
|  | cluster_2 | 1 | matrix-clustering_query_matrices.tab_1::3.1039 | 3.1039 : 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
Display Logo Trees
cluster_1
cluster_2
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | v T T w y T b |  |  | 3.1039::2_motifs | PSSM | 5.51 | 2000
Node 2 | v T T w y T b |  |  | 3.1039::3_motifs | PSSM | 5.51 | 3000

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | a G T C y T G C T v C T s |  |  | 3.1039 : 1 motif | PSSM | 10.22 | 999

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3.1039_m2_matrix-clustering_query_matrices.tab_2 | matrix-clustering_query_matrices.tab_2 | cluster_1 | 3.1039 | 7 | 5.51 | 1000 | v T T w y T b | V A R W A A B |  |
3.1039_m4_matrix-clustering_query_matrices.tab_4 | matrix-clustering_query_matrices.tab_4 | cluster_1 | 3.1039 | 7 | 5.51 | 1000 | V A R W A A B | v T T w y T b |  |
3.1039_m3_matrix-clustering_query_matrices.tab_3 | matrix-clustering_query_matrices.tab_3 | cluster_1 | 3.1039 | 7 | 5.51 | 1000 | v T T w y T b | V A R W A A B |  |
3.1039_m1_matrix-clustering_query_matrices.tab_1 | matrix-clustering_query_matrices.tab_1 | cluster_2 | 3.1039 | 13 | 10.22 | 999 | a G T C y T G C T v C T s | S A G B A G C A R G A C T |  |
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