# RSAT - matrix-clustering result

### Analysis: oct4_motifs_found_in_chen_2008_peak_sets (24/02/2025 10:03)

## 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
22 | 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 | 15 | positions_8nt_m2::oct4_peak_motifs:: positions_7nt_m1::oct4_peak_motifs:: oligos_7nt_mkv5_m2::oct4_peak_motifs:: local_words_7nt_m3::oct4_peak_motifs:: local_words_8nt_m3::oct4_peak_motifs:: oligos_7nt_mkv5_m1::oct4_peak_motifs:: positions_8nt_m4::oct4_peak_motifs:: oligos_7nt_mkv5_m4::oct4_peak_motifs:: local_words_7nt_m4::oct4_peak_motifs:: positions_8nt_m1::oct4_peak_motifs:: local_words_8nt_m1::oct4_peak_motifs:: local_words_8nt_m2::oct4_peak_motifs:: positions_7nt_m2::oct4_peak_motifs:: local_words_7nt_m1::oct4_peak_motifs:: local_words_7nt_m2::oct4_peak_motifs:: | oct4_peak_motifs::15_motifs | Show matrix
|  | cluster_2 | 4 | oligos_8nt_mkv6_m3::oct4_peak_motifs:: oligos_8nt_mkv6_m4::oct4_peak_motifs:: oligos_8nt_mkv6_m1::oct4_peak_motifs:: oligos_8nt_mkv6_m2::oct4_peak_motifs:: | oct4_peak_motifs::4_motifs | Show matrix
|  | cluster_3 | 2 | positions_7nt_m4::oct4_peak_motifs:: positions_8nt_m3::oct4_peak_motifs:: | oct4_peak_motifs::2_motifs | Show matrix
|  | cluster_4 | 1 | oligos_7nt_mkv5_m3::oct4_peak_motifs | oct4_peak_motifs : 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 | --s y w T T g T T A T G C A A A T d w---- |  |  | oct4_peak_motifs::2_motifs | PSSM | 9.43 | 1487
Node 2 | --s y w T T g T t A T G C A A A t d w---- |  |  | oct4_peak_motifs::2_motifs | PSSM | 9.31 | 1609
Node 3 | --s y w T T g T t A T G C A A A t d w---- |  |  | oct4_peak_motifs::3_motifs | PSSM | 9.32 | 2390
Node 4 | --s y w T T g T t A T G C A A A t d w---- |  |  | oct4_peak_motifs::5_motifs | PSSM | 9.36 | 3877
Node 5 | --s y w T T g T t A T G C A A A t k w m--- |  |  | oct4_peak_motifs::6_motifs | PSSM | 9.45 | 4425
Node 6 | --------w t A T G C A w A T k h---- |  |  | oct4_peak_motifs::2_motifs | PSSM | 7.19 | 1997
Node 7 | ------w s a t A T G C A w A T g h---- |  |  | oct4_peak_motifs::3_motifs | PSSM | 7.22 | 3080
Node 8 | w y a y w T G C A T A T G C A w r t r w---- |  |  | oct4_peak_motifs::2_motifs | PSSM | 8.70 | 790
Node 9 | --y y a T T G T y A T G y w--------- |  |  | oct4_peak_motifs::2_motifs | PSSM | 7.31 | 1333
Node 10 | ------w s a t A T G C w a A T k h---- |  |  | oct4_peak_motifs::4_motifs | PSSM | 6.52 | 4580
Node 11 | --s y w T T g T t A T G C A A A t k w a t r m |  |  | oct4_peak_motifs::7_motifs | PSSM | 9.68 | 4616
Node 12 | --s y w T T g T t A T G c A A A t k w a t r m |  |  | oct4_peak_motifs::9_motifs | PSSM | 9.46 | 5949
Node 13 | --s y w T T g w t A T G C A A A t k w a t r m |  |  | oct4_peak_motifs::13_motifs | PSSM | 8.94 | 10529
Node 14 | w y c y w T T g w t A T G C A a A t k w a t r m |  |  | oct4_peak_motifs::15_motifs | PSSM | 8.62 | 11319

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | y g C G C A k G C G c r |  |  | oct4_peak_motifs::2_motifs | PSSM | 7.51 | 1815
Node 2 | s g C G C A g s C G c s |  |  | oct4_peak_motifs::3_motifs | PSSM | 6.93 | 2696
Node 3 | s g C G C A g G C G c s |  |  | oct4_peak_motifs::4_motifs | PSSM | 6.30 | 3370

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | g y a T A T G C G C A T A t r c |  |  | oct4_peak_motifs::2_motifs | PSSM | 7.99 | 732

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | s s C G C C C T C s s |  |  | oct4_peak_motifs : 1 motif | PSSM | 6.53 | 1681

- 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_m21_positions_8nt_m3 | positions_8nt_m3 | cluster_3 | oct4_peak_motifs | 16 | 8.25 | 335 | G C A T A T G C G C A T A T G C | g c a T A T G C G C A T A t g c |  |
oct4_peak_motifs_m17_local_words_8nt_m2 | local_words_8nt_m2 | cluster_1 | oct4_peak_motifs | 24 | 9.43 | 743 | ++S Y W T T G T T A T G C A A A T D W++++ | ++++w h A T T T G C A T A A c A A w r s++ |  |
oct4_peak_motifs_m1_oligos_7nt_mkv5_m1 | oligos_7nt_mkv5_m1 | cluster_1 | oct4_peak_motifs | 24 | 7.64 | 1053 | ++++++++w w A T G C A A A T g w++++ | ++++W C A T T T G C A T W W++++++++ |  |
oct4_peak_motifs_m11_positions_7nt_m4 | positions_7nt_m4 | cluster_3 | oct4_peak_motifs | 16 | 7.88 | 397 | +y a T A T G C G C A T A t r+ | +Y A T A T G C G C A T A T R+ |  |
oct4_peak_motifs_m19_positions_8nt_m1 | positions_8nt_m1 | cluster_1 | oct4_peak_motifs | 24 | 10.11 | 548 | ++s y a T T g T t A T G C A A A T g w m+++ | +++K W C A T T T G C A T A A C A A T R S++ |  |
oct4_peak_motifs_m6_local_words_7nt_m2 | local_words_7nt_m2 | cluster_1 | oct4_peak_motifs | 24 | 9.31 | 803 | ++S Y W T T G T T A T G C A A A T D W++++ | ++++w h a T T T G C A T a A c A A w r s++ |  |
oct4_peak_motifs_m5_local_words_7nt_m1 | local_words_7nt_m1 | cluster_1 | oct4_peak_motifs | 24 | 9.30 | 806 | ++s y w T T g T t A T G C A A A t d w++++ | ++++W H A T T T G C A T A A C A A W R S++ |  |
oct4_peak_motifs_m12_oligos_8nt_mkv6_m1 | oligos_8nt_mkv6_m1 | cluster_2 | oct4_peak_motifs | 12 | 7.44 | 1056 | s g C G C A G G C G s s | S S C G C C T G C G C S |  |
oct4_peak_motifs_m13_oligos_8nt_mkv6_m2 | oligos_8nt_mkv6_m2 | cluster_2 | oct4_peak_motifs | 12 | 8.33 | 759 | y g C G C a t G C G c r | Y G C G C A T G C G C R |  |
oct4_peak_motifs_m15_oligos_8nt_mkv6_m4 | oligos_8nt_mkv6_m4 | cluster_2 | oct4_peak_motifs | 12 | 7.47 | 881 | S S C G G C T G C G S S | s s C G C A G C C G s s |  |
oct4_peak_motifs_m7_local_words_7nt_m3 | local_words_7nt_m3 | cluster_1 | oct4_peak_motifs | 24 | 7.58 | 1083 | ++++++W C A T T T G C A T A T S W++++ | ++++w s A T A T G C A A A T g w++++++ |  |
oct4_peak_motifs_m14_oligos_8nt_mkv6_m3 | oligos_8nt_mkv6_m3 | cluster_2 | oct4_peak_motifs | 12 | 7.34 | 674 | S S C G G A A G C G S S | s s C G C T T C C G s s |  |
oct4_peak_motifs_m18_local_words_8nt_m3 | local_words_8nt_m3 | cluster_1 | oct4_peak_motifs | 24 | 7.34 | 944 | ++++++++W Y A T G C A T A T K H++++ | ++++d m A T A T G C A T r w++++++++ |  |
oct4_peak_motifs_m3_oligos_7nt_mkv5_m3 | oligos_7nt_mkv5_m3 | cluster_4 | oct4_peak_motifs | 11 | 6.53 | 1681 | s s C G C C C T C s s | S S G A G G G C G S S |  |
oct4_peak_motifs_m16_local_words_8nt_m1 | local_words_8nt_m1 | cluster_1 | oct4_peak_motifs | 24 | 9.43 | 744 | ++s y w T T g T T A T G C A A A T d w++++ | ++++W H A T T T G C A T A A C A A W R S++ |  |
oct4_peak_motifs_m8_local_words_7nt_m4 | local_words_7nt_m4 | cluster_1 | oct4_peak_motifs | 24 | 10.02 | 191 | ++K Y A T T G T T A T G C A T A A C A A T R M | k y a T T g T T a T G C A t A A c A A t r m++ |  |
oct4_peak_motifs_m9_positions_7nt_m1 | positions_7nt_m1 | cluster_1 | oct4_peak_motifs | 24 | 10.18 | 285 | w y a T t T g C A T A T G c A a A t r w++++ | ++++W Y A T T T G C A T A T G C A A A T R W |  |
oct4_peak_motifs_m4_oligos_7nt_mkv5_m4 | oligos_7nt_mkv5_m4 | cluster_1 | oct4_peak_motifs | 24 | 7.56 | 655 | ++Y Y A T T G T T A T K Y++++++++++ | ++++++++++r m A T A A C A A T r r++ |  |
oct4_peak_motifs_m2_oligos_7nt_mkv5_m2 | oligos_7nt_mkv5_m2 | cluster_1 | oct4_peak_motifs | 24 | 6.43 | 1500 | ++++++++A A T T A G C A T W W+++++ | +++++w w A T G C T A A t t++++++++ |  |
oct4_peak_motifs_m20_positions_8nt_m2 | positions_8nt_m2 | cluster_1 | oct4_peak_motifs | 24 | 8.84 | 505 | +Y A Y A T G C A T A T G C A T R T R+++++ | +++++y a y A T G C A T A T G C A T r t r+ |  |
oct4_peak_motifs_m10_positions_7nt_m2 | positions_7nt_m2 | cluster_1 | oct4_peak_motifs | 24 | 9.36 | 781 | ++S Y W T T G T T A T G C A A A T D W++++ | ++++w h a T T T G C A T a A c A A w r s++ |  |
oct4_peak_motifs_m22_positions_8nt_m4 | positions_8nt_m4 | cluster_1 | oct4_peak_motifs | 24 | 7.98 | 678 | +++Y W T T G T C A T G Y W+++++++++ | +++++++++w r C A T G A C A A w r+++ |  |
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