# RSAT - matrix-clustering result

### Analysis: wt_top1 (30/05/2025 13:41)

## 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
32 | 1 | 22 | 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 cluster_18 cluster_19 cluster_20 cluster_21 cluster_22
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 | homer_23.CACTCACCAGGG::wt_top1:: homer_14.ACACCCGCAA::wt_top1:: homer_15.CTGCCSGCAAGG::wt_top1:: | wt_top1::3_motifs | Show matrix
|  | cluster_2 | 1 | homer_7.GGGAAGCAGCCT::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_3 | 1 | homer_9.RGATGGCGDCCG::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_4 | 2 | homer_28.TGCCCCAA::wt_top1:: homer_2.TGCGCCAGAT::wt_top1:: | wt_top1::2_motifs | Show matrix
|  | cluster_5 | 2 | homer_10.CCYAANCCAA::wt_top1:: homer_20.TCTGGAACGGGC::wt_top1:: | wt_top1::2_motifs | Show matrix
|  | cluster_6 | 2 | homer_29.AGAGBGTCRCAG::wt_top1:: homer_30.GAGTCGCGGA::wt_top1:: | wt_top1::2_motifs | Show matrix
|  | cluster_7 | 2 | homer_25.TGCGGTAC::wt_top1:: homer_5.CGCGGAACTT::wt_top1:: | wt_top1::2_motifs | Show matrix
|  | cluster_8 | 1 | homer_1.GGGCACMTGYCC::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_9 | 1 | homer_13.GTGGWCCGSAGA::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_10 | 2 | homer_18.AGTCTTGCCC::wt_top1:: homer_31.ACGGGCGATA::wt_top1:: | wt_top1::2_motifs | Show matrix
|  | cluster_11 | 2 | homer_21.MAGCCTCAGCAG::wt_top1:: homer_32.CASAGSCAGAGS::wt_top1:: | wt_top1::2_motifs | Show matrix
|  | cluster_12 | 3 | homer_26.CTAAGACC::wt_top1:: homer_19.ATTAGTCTGA::wt_top1:: homer_24.GGACCAMGAT::wt_top1:: | wt_top1::3_motifs | Show matrix
|  | cluster_13 | 1 | homer_12.WCSGGACY::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_14 | 1 | homer_27.ATAGGGAA::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_15 | 1 | homer_22.TCTAACCTGTTC::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_16 | 1 | homer_3.GGTRGCCKGCTK::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_17 | 1 | homer_17.AAGCACAGTG::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_18 | 1 | homer_6.ACCRGCKGTC::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_19 | 1 | homer_8.ATCCCGTGTGGG::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_20 | 1 | homer_11.GGGCCTGCACTG::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_21 | 1 | homer_4.NGGAAMTTAGKG::wt_top1 | wt_top1 : 1 motif | Show matrix
|  | cluster_22 | 1 | homer_16.RCTCGAGTCKVG::wt_top1 | wt_top1 : 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

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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
cluster_18
cluster_19
cluster_20
cluster_21
cluster_22
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
cluster_18
cluster_19
cluster_20
cluster_21
cluster_22
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | m y r C c s G c A A G G- |  |  | wt_top1::2_motifs | PSSM | 5.88 | 201
Node 2 | m c a C y C r C m A G G G |  |  | wt_top1::3_motifs | PSSM | 8.17 | 301

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G G G A A G C A G C C T |  |  | wt_top1 : 1 motif | PSSM | 5.68 | 101

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | R G A T G G C G D C C G |  |  | wt_top1 : 1 motif | PSSM | 10.69 | 100

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | T G C s c C A r A T |  |  | wt_top1::2_motifs | PSSM | 7.25 | 200

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | G C C y r w k C C A r A |  |  | wt_top1::2_motifs | PSSM | 6.63 | 201

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A G A G a r T C g C r G A |  |  | wt_top1::2_motifs | PSSM | 13.50 | 200

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | y G C g G w A C T T |  |  | wt_top1::2_motifs | PSSM | 7.50 | 200

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G G G C A C M T G Y C C |  |  | wt_top1 : 1 motif | PSSM | 10.53 | 101

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G T G G W C C G S A G A |  |  | wt_top1 : 1 motif | PSSM | 10.05 | 101

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A G T m T y G C C C G T |  |  | wt_top1::2_motifs | PSSM | 13.55 | 200

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | c a m A G y C w s A G c A G |  |  | wt_top1::2_motifs | PSSM | 8.10 | 201

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A T m k T r G T C c g A- |  |  | wt_top1::2_motifs | PSSM | 8.87 | 201
Node 2 | A T m k T r G T C y k A G |  |  | wt_top1::3_motifs | PSSM | 8.42 | 301

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | W C S G G A C Y |  |  | wt_top1 : 1 motif | PSSM | 7.33 | 100

cluster_14

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A T A G G G A A |  |  | wt_top1 : 1 motif | PSSM | 3.57 | 100

cluster_15

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T C T A A C C T G T T C |  |  | wt_top1 : 1 motif | PSSM | 6.75 | 101

cluster_16

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G G T R G C C K G C T K |  |  | wt_top1 : 1 motif | PSSM | 11.58 | 100

cluster_17

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A A G C A C A G T G |  |  | wt_top1 : 1 motif | PSSM | 6.55 | 101

cluster_18

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A C C R G C K G T C |  |  | wt_top1 : 1 motif | PSSM | 5.98 | 101

cluster_19

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | A T C C C G T G T G G G |  |  | wt_top1 : 1 motif | PSSM | 11.65 | 100

cluster_20

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G G G C C T G C A C T G |  |  | wt_top1 : 1 motif | PSSM | 10.01 | 101

cluster_21

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | N G G A A M T T A G K G |  |  | wt_top1 : 1 motif | PSSM | 3.56 | 101

cluster_22

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | R C T C G A G T C K V G |  |  | wt_top1 : 1 motif | PSSM | 7.70 | 100

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
wt_top1_m29_homer_29.AGAGBGTCRCAG | homer_29.AGAGBGTCRCAG | cluster_6 | wt_top1 | 13 | 12.39 | 100 | A G A G t G T C r C A G+ | +C T G Y G A C A C T C T |  |
wt_top1_m27_homer_27.ATAGGGAA | homer_27.ATAGGGAA | cluster_14 | wt_top1 | 8 | 3.57 | 100 | A T A G G G A A | T T C C C T A T |  |
wt_top1_m12_homer_12.WCSGGACY | homer_12.WCSGGACY | cluster_13 | wt_top1 | 8 | 7.33 | 100 | w m s G G A C y | R G T C C S K W |  |
wt_top1_m32_homer_32.CASAGSCAGAGS | homer_32.CASAGSCAGAGS | cluster_11 | wt_top1 | 14 | 3.77 | 101 | c a s A g s c a s a g s++ | ++S C T S T G S C T S T G |  |
wt_top1_m6_homer_6.ACCRGCKGTC | homer_6.ACCRGCKGTC | cluster_18 | wt_top1 | 10 | 5.98 | 101 | a C C r G C k G T C | G A C M G C Y G G T |  |
wt_top1_m23_homer_23.CACTCACCAGGG | homer_23.CACTCACCAGGG | cluster_1 | wt_top1 | 13 | 14.37 | 100 | +C C C T G G T G R G T G | C A C Y C A C C A G G G+ |  |
wt_top1_m9_homer_9.RGATGGCGDCCG | homer_9.RGATGGCGDCCG | cluster_3 | wt_top1 | 12 | 10.69 | 100 | r G A w G S y G r C C k | M G G Y C R S C W T C Y |  |
wt_top1_m30_homer_30.GAGTCGCGGA | homer_30.GAGTCGCGGA | cluster_6 | wt_top1 | 13 | 12.01 | 100 | +++G A r T C s C G G A | T C C G S G A Y T C+++ |  |
wt_top1_m14_homer_14.ACACCCGCAA | homer_14.ACACCCGCAA | cluster_1 | wt_top1 | 13 | 4.46 | 100 | A C A C C C G C A A+++ | +++T T G C G G G T G T |  |
wt_top1_m2_homer_2.TGCGCCAGAT | homer_2.TGCGCCAGAT | cluster_4 | wt_top1 | 10 | 11.31 | 100 | T G C G m C A G A T | A T C T G K C G C A |  |
wt_top1_m22_homer_22.TCTAACCTGTTC | homer_22.TCTAACCTGTTC | cluster_15 | wt_top1 | 12 | 6.75 | 101 | T C T a A C C T G T T C | G A A C A G G T T A G A |  |
wt_top1_m3_homer_3.GGTRGCCKGCTK | homer_3.GGTRGCCKGCTK | cluster_16 | wt_top1 | 12 | 11.58 | 100 | G k T r G C Y k G C T k | M A G C M R G C Y A M C |  |
wt_top1_m4_homer_4.NGGAAMTTAGKG | homer_4.NGGAAMTTAGKG | cluster_21 | wt_top1 | 12 | 3.56 | 101 | m G G w A m w t A g k g | C M C T A W K T W C C K |  |
wt_top1_m1_homer_1.GGGCACMTGYCC | homer_1.GGGCACMTGYCC | cluster_8 | wt_top1 | 12 | 10.53 | 101 | G G r C A C m w G y C C | G G R C W K G T G Y C C |  |
wt_top1_m17_homer_17.AAGCACAGTG | homer_17.AAGCACAGTG | cluster_17 | wt_top1 | 10 | 6.55 | 101 | r r k C A C w G t G | C A C W G T G M Y Y |  |
wt_top1_m11_homer_11.GGGCCTGCACTG | homer_11.GGGCCTGCACTG | cluster_20 | wt_top1 | 12 | 10.01 | 101 | G G G C m k G m w C T G | C A G W K C M K G C C C |  |
wt_top1_m31_homer_31.ACGGGCGATA | homer_31.ACGGGCGATA | cluster_10 | wt_top1 | 12 | 10.48 | 100 | ++T A T C G C C C G T | A C G G G C G A T A++ |  |
wt_top1_m28_homer_28.TGCCCCAA | homer_28.TGCCCCAA | cluster_4 | wt_top1 | 10 | 3.57 | 100 | T G C C C C A A++ | ++T T G G G G C A |  |
wt_top1_m15_homer_15.CTGCCSGCAAGG | homer_15.CTGCCSGCAAGG | cluster_1 | wt_top1 | 13 | 7.71 | 101 | m k r C y s G s A A G G+ | +C C T T S C S R G Y M K |  |
wt_top1_m16_homer_16.RCTCGAGTCKVG | homer_16.RCTCGAGTCKVG | cluster_22 | wt_top1 | 12 | 7.70 | 100 | r C T C G A S y C k v s | S B M G R S T C G A G Y |  |
wt_top1_m18_homer_18.AGTCTTGCCC | homer_18.AGTCTTGCCC | cluster_10 | wt_top1 | 12 | 13.81 | 100 | A G T C T T G C C C++ | ++G G G C A A G A C T |  |
wt_top1_m20_homer_20.TCTGGAACGGGC | homer_20.TCTGGAACGGGC | cluster_5 | wt_top1 | 12 | 7.49 | 100 | G C C Y G T K C C A G A | T c T G G m A C r G G C |  |
wt_top1_m8_homer_8.ATCCCGTGTGGG | homer_8.ATCCCGTGTGGG | cluster_19 | wt_top1 | 12 | 11.65 | 100 | R y C C C G w G T G G r | Y C C A C W C G G G R Y |  |
wt_top1_m21_homer_21.MAGCCTCAGCAG | homer_21.MAGCCTCAGCAG | cluster_11 | wt_top1 | 14 | 12.75 | 100 | ++m A G y C w C A G C A G | C T G C T G W G R C T K++ |  |
wt_top1_m19_homer_19.ATTAGTCTGA | homer_19.ATTAGTCTGA | cluster_12 | wt_top1 | 13 | 5.16 | 101 | ++m T T r G t C y g A+ | +T C R G A C Y A A K++ |  |
wt_top1_m5_homer_5.CGCGGAACTT | homer_5.CGCGGAACTT | cluster_7 | wt_top1 | 10 | 12.52 | 100 | C G C s G A A C T T | A A G T T C S G C G |  |
wt_top1_m26_homer_26.CTAAGACC | homer_26.CTAAGACC | cluster_12 | wt_top1 | 13 | 3.57 | 100 | +++++G G T C T T A G | C T A A G A C C+++++ |  |
wt_top1_m25_homer_25.TGCGGTAC | homer_25.TGCGGTAC | cluster_7 | wt_top1 | 10 | 3.57 | 100 | T G C G G T A C++ | ++G T A C C G C A |  |
wt_top1_m10_homer_10.CCYAANCCAA | homer_10.CCYAANCCAA | cluster_5 | wt_top1 | 12 | 6.71 | 101 | +C C y A A v C C w m+ | +K W G G B T T R G G+ |  |
wt_top1_m13_homer_13.GTGGWCCGSAGA | homer_13.GTGGWCCGSAGA | cluster_9 | wt_top1 | 12 | 10.05 | 101 | G y G G d C C G s r G A | T C Y S C G G H C C R C |  |
wt_top1_m7_homer_7.GGGAAGCAGCCT | homer_7.GGGAAGCAGCCT | cluster_2 | wt_top1 | 12 | 5.68 | 101 | R G r A r k c r g y C T | A G R C Y G M Y T Y C Y |  |
wt_top1_m24_homer_24.GGACCAMGAT | homer_24.GGACCAMGAT | cluster_12 | wt_top1 | 13 | 11.58 | 100 | A T C K T R R T C C+++ | +++G G A Y y A m G A 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