# RSAT - matrix-clustering result

### Analysis: clustering_column-permuted_matrices_discovered_in_oct4_chip-seq (11/05/2026 05:37)

## 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
21 | 1 | 17 | 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 cluster_7 cluster_8 cluster_9 cluster_10 cluster_11 cluster_12 cluster_13 cluster_14 cluster_15 cluster_16 cluster_17
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 | 2 | positions_7nt_m3_perm1::oct4_peak_motifs_permuted:: positions_6nt_m2_perm1::oct4_peak_motifs_permuted:: | oct4_peak_motifs_permuted::2_motifs | Show matrix
|  | cluster_2 | 2 | dyads_m1_perm1::oct4_peak_motifs_permuted:: dyads_m2_perm1::oct4_peak_motifs_permuted:: | oct4_peak_motifs_permuted::2_motifs | Show matrix
|  | cluster_3 | 2 | local_words_6nt_m2_perm1::oct4_peak_motifs_permuted:: positions_6nt_m1_perm1::oct4_peak_motifs_permuted:: | oct4_peak_motifs_permuted::2_motifs | Show matrix
|  | cluster_4 | 1 | oligos_7nt_mkv5_m3_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_5 | 1 | oligos_7nt_mkv5_m1_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_6 | 1 | oligos_7nt_mkv5_m2_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_7 | 2 | local_words_7nt_m3_perm1::oct4_peak_motifs_permuted:: dyads_m3_perm1::oct4_peak_motifs_permuted:: | oct4_peak_motifs_permuted::2_motifs | Show matrix
|  | cluster_8 | 1 | oligos_6nt_mkv4_m2_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_9 | 1 | oligos_6nt_mkv4_m3_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_10 | 1 | local_words_7nt_m2_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_11 | 1 | positions_7nt_m1_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_12 | 1 | oligos_6nt_mkv4_m1_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_13 | 1 | local_words_7nt_m1_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_14 | 1 | positions_7nt_m2_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_15 | 1 | local_words_6nt_m3_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_16 | 1 | local_words_6nt_m1_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 1 motif | Show matrix
|  | cluster_17 | 1 | positions_6nt_m3_perm1::oct4_peak_motifs_permuted | oct4_peak_motifs_permuted : 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
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cluster_1
cluster_2
cluster_3
cluster_4
cluster_5
cluster_6
cluster_7
cluster_8
cluster_9
cluster_10
cluster_11
cluster_12
cluster_13
cluster_14
cluster_15
cluster_16
cluster_17
Display Logo Trees
cluster_1
cluster_2
cluster_3
cluster_4
cluster_5
cluster_6
cluster_7
cluster_8
cluster_9
cluster_10
cluster_11
cluster_12
cluster_13
cluster_14
cluster_15
cluster_16
cluster_17
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | a A A A a A A a a A A |  |  | oct4_peak_motifs_permuted::2_motifs | PSSM | 10.42 | 4226

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | C C g r C s s C s C C C C C |  |  | oct4_peak_motifs_permuted::2_motifs | PSSM | 11.08 | 1039

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | C C t w r w T T c G T w w A C w w A A |  |  | oct4_peak_motifs_permuted::2_motifs | PSSM | 9.76 | 2197

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T A T A r r A r A m r m |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 9.84 | 839

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w A w G k T w T A w R Y |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 9.58 | 2583

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G A t w k w A A y w T |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 8.79 | 3774

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | T C A y G G r T r A y T A c a T |  |  | oct4_peak_motifs_permuted::2_motifs | PSSM | 10.40 | 1076

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T C y s A s r G C G |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 7.80 | 992

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | r T m A C C G y G k |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 8.62 | 1974

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y w C C T T a r A T v A w A c w T A r |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 10.25 | 1368

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G G w T t W A w T T w A G r A y y C T |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 12.71 | 729

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T w b T Y w K h g T w W A |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 9.38 | 2192

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T w A y y T A w a T T T G w g y T A G |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 10.00 | 1033

cluster_14

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A A T T y A r r G T T G y G y C C A w y A |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 13.24 | 223

cluster_15

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y G r T G T C A C A r y |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 8.60 | 1291

cluster_16

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T y T c w k A G T w T w t T w w c G A |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 10.15 | 1028

cluster_17

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y r y A r G T T C G A T C C r T w T A |  |  | oct4_peak_motifs_permuted : 1 motif | PSSM | 12.69 | 157

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
oct4_peak_motifs_permuted_m12_oligos_7nt_mkv5_m3_perm1 | oligos_7nt_mkv5_m3_perm1 | cluster_4 | oct4_peak_motifs_permuted | 12 | 9.84 | 839 | T A T A r r A r A m r m | K Y K T Y T Y Y T A T A |  |
oct4_peak_motifs_permuted_m13_local_words_7nt_m1_perm1 | local_words_7nt_m1_perm1 | cluster_13 | oct4_peak_motifs_permuted | 19 | 10.00 | 1033 | T w A y y T A w a T T T G w g y T A G | C T A R C W C A A A T W T A R R T W A |  |
oct4_peak_motifs_permuted_m18_positions_7nt_m3_perm1 | positions_7nt_m3_perm1 | cluster_1 | oct4_peak_motifs_permuted | 11 | 10.95 | 3939 | a A A A a A A A A A A | T T T T T T T T T T T |  |
oct4_peak_motifs_permuted_m8_positions_6nt_m2_perm1 | positions_6nt_m2_perm1 | cluster_1 | oct4_peak_motifs_permuted | 11 | 7.87 | 287 | A w A A w A a t w A+ | +T W A T T W T T W T |  |
oct4_peak_motifs_permuted_m21_dyads_m3_perm1 | dyads_m3_perm1 | cluster_7 | oct4_peak_motifs_permuted | 16 | 12.03 | 269 | ++A C c s g T A A w T A w a T | A T W T A W T T A C S G G T++ |  |
oct4_peak_motifs_permuted_m2_oligos_6nt_mkv4_m2_perm1 | oligos_6nt_mkv4_m2_perm1 | cluster_8 | oct4_peak_motifs_permuted | 10 | 7.80 | 992 | T C y s A s r G C G | C G C Y S T S R G A |  |
oct4_peak_motifs_permuted_m1_oligos_6nt_mkv4_m1_perm1 | oligos_6nt_mkv4_m1_perm1 | cluster_12 | oct4_peak_motifs_permuted | 13 | 9.38 | 2192 | T w b T Y w K h g T w W A | T W W A C D M W R A V W A |  |
oct4_peak_motifs_permuted_m7_positions_6nt_m1_perm1 | positions_6nt_m1_perm1 | cluster_3 | oct4_peak_motifs_permuted | 19 | 10.08 | 1428 | ++++g h T t c G T w T w C t W A A | T T W A G W A W A C G A A D C++++ |  |
oct4_peak_motifs_permuted_m4_local_words_6nt_m1_perm1 | local_words_6nt_m1_perm1 | cluster_16 | oct4_peak_motifs_permuted | 19 | 10.15 | 1028 | T y T c w k A G T w T w t T w w c G A | T C G W W A A W A W A C T M W G A R A |  |
oct4_peak_motifs_permuted_m3_oligos_6nt_mkv4_m3_perm1 | oligos_6nt_mkv4_m3_perm1 | cluster_9 | oct4_peak_motifs_permuted | 10 | 8.62 | 1974 | r T m A C C G y G k | M C R C G G T K A Y |  |
oct4_peak_motifs_permuted_m17_positions_7nt_m2_perm1 | positions_7nt_m2_perm1 | cluster_14 | oct4_peak_motifs_permuted | 21 | 13.24 | 223 | A A T T y A r r G T T G y G y C C A w y A | T R W T G G R C R C A A C Y Y T R A A T T |  |
oct4_peak_motifs_permuted_m9_positions_6nt_m3_perm1 | positions_6nt_m3_perm1 | cluster_17 | oct4_peak_motifs_permuted | 19 | 12.69 | 157 | y r y A r G T T C G A T C C r T w T A | T A W A Y G G A T C G A A C Y T R Y R |  |
oct4_peak_motifs_permuted_m16_positions_7nt_m1_perm1 | positions_7nt_m1_perm1 | cluster_11 | oct4_peak_motifs_permuted | 19 | 12.71 | 729 | G G w T t W A w T T w A G r A y y C T | A G R R T Y C T W A A W T W A A W C C |  |
oct4_peak_motifs_permuted_m11_oligos_7nt_mkv5_m2_perm1 | oligos_7nt_mkv5_m2_perm1 | cluster_6 | oct4_peak_motifs_permuted | 11 | 8.79 | 3774 | G A t w k w A A y w T | A W R T T W M W A T C |  |
oct4_peak_motifs_permuted_m5_local_words_6nt_m2_perm1 | local_words_6nt_m2_perm1 | cluster_3 | oct4_peak_motifs_permuted | 19 | 10.07 | 769 | C C t w r r T T w g T w A A m a w A A | T T W T K T T W A C W A A Y Y W A G G |  |
oct4_peak_motifs_permuted_m19_dyads_m1_perm1 | dyads_m1_perm1 | cluster_2 | oct4_peak_motifs_permuted | 14 | 11.96 | 604 | C C G G C s s C g c C c c C | G G G G G C G S S G C C G G |  |
oct4_peak_motifs_permuted_m15_local_words_7nt_m3_perm1 | local_words_7nt_m3_perm1 | cluster_7 | oct4_peak_motifs_permuted | 16 | 9.51 | 807 | T C A y G G r T g A c T A C++ | ++G T A G T C A Y C C R T G A |  |
oct4_peak_motifs_permuted_m20_dyads_m2_perm1 | dyads_m2_perm1 | cluster_2 | oct4_peak_motifs_permuted | 14 | 13.37 | 435 | +C c A C m C C c C C C C C | G G G G G G G G K G T G G+ |  |
oct4_peak_motifs_permuted_m14_local_words_7nt_m2_perm1 | local_words_7nt_m2_perm1 | cluster_10 | oct4_peak_motifs_permuted | 19 | 10.25 | 1368 | y w C C T T a r A T v A w A c w T A r | Y T A W G T W T B A T Y T A A G G W R |  |
oct4_peak_motifs_permuted_m6_local_words_6nt_m3_perm1 | local_words_6nt_m3_perm1 | cluster_15 | oct4_peak_motifs_permuted | 12 | 8.60 | 1291 | y G r T G T C A C A r y | R Y T G T G A C A Y C R |  |
oct4_peak_motifs_permuted_m10_oligos_7nt_mkv5_m1_perm1 | oligos_7nt_mkv5_m1_perm1 | cluster_5 | oct4_peak_motifs_permuted | 12 | 9.58 | 2583 | w A w G k T w T A w R Y | R Y W T A W A M C W T W |  |
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