# RSAT - matrix-clustering result

### Analysis: jan06 (06/01/2025 09:58)

## 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 | 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 | 3 | matrix-clustering_query_matrices.tab_6::1.2096:: matrix-clustering_query_matrices.tab_2::1.2096:: matrix-clustering_query_matrices.tab_4::1.2096:: | 1.2096::3_motifs | Show matrix
|  | cluster_2 | 3 | matrix-clustering_query_matrices.tab_1::1.2096:: matrix-clustering_query_matrices.tab_3::1.2096:: matrix-clustering_query_matrices.tab_5::1.2096:: | 1.2096::3_motifs | Show matrix
|  | cluster_3 | 1 | matrix-clustering_query_matrices.tab_7::1.2096 | 1.2096 : 1 motif | Show matrix
|  | cluster_4 | 1 | matrix-clustering_query_matrices.tab_8::1.2096 | 1.2096 : 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
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | v T T C G y G y T T |  |  | 1.2096::2_motifs | PSSM | 9.77 | 2000
Node 2 | v T T C G y G y T T |  |  | 1.2096::3_motifs | PSSM | 9.77 | 3000

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A T T C G k G C G C y G s |  |  | 1.2096::2_motifs | PSSM | 13.97 | 2000
Node 2 | A T T C G k G C G C y G s |  |  | 1.2096::3_motifs | PSSM | 13.85 | 3000

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G y G k G T G C T T |  |  | 1.2096 : 1 motif | PSSM | 12.20 | 999

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | v T G s C Y w |  |  | 1.2096 : 1 motif | PSSM | 5.37 | 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1.2096_m2_matrix-clustering_query_matrices.tab_2 | matrix-clustering_query_matrices.tab_2 | cluster_1 | 1.2096 | 10 | 9.77 | 1000 | v T T C G y G y T T | A A R C R C G A A B |  |
1.2096_m4_matrix-clustering_query_matrices.tab_4 | matrix-clustering_query_matrices.tab_4 | cluster_1 | 1.2096 | 10 | 9.77 | 1000 | v T T C G y G y T T | A A R C R C G A A B |  |
1.2096_m7_matrix-clustering_query_matrices.tab_7 | matrix-clustering_query_matrices.tab_7 | cluster_3 | 1.2096 | 10 | 12.20 | 999 | G y G k G T G C T T | A A G C A C M C R C |  |
1.2096_m5_matrix-clustering_query_matrices.tab_5 | matrix-clustering_query_matrices.tab_5 | cluster_2 | 1.2096 | 13 | 13.97 | 1000 | A T T C G k G C G C y G s | S C R G C G C M C G A A T |  |
1.2096_m6_matrix-clustering_query_matrices.tab_6 | matrix-clustering_query_matrices.tab_6 | cluster_1 | 1.2096 | 10 | 9.77 | 1000 | A A R C R C G A A B | v T T C G y G y T T |  |
1.2096_m3_matrix-clustering_query_matrices.tab_3 | matrix-clustering_query_matrices.tab_3 | cluster_2 | 1.2096 | 13 | 13.97 | 1000 | A T T C G k G C G C y G s | S C R G C G C M C G A A T |  |
1.2096_m1_matrix-clustering_query_matrices.tab_1 | matrix-clustering_query_matrices.tab_1 | cluster_2 | 1.2096 | 13 | 11.15 | 1000 | G C G C M C G A A T+++ | +++A T T C G k G C G C |  |
1.2096_m8_matrix-clustering_query_matrices.tab_8 | matrix-clustering_query_matrices.tab_8 | cluster_4 | 1.2096 | 7 | 5.37 | 999 | v T G s C Y w | W R G S C A B |  |
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