# RSAT - matrix-clustering result

### Analysis: hsc_lincorr_baso (09/04/2026 19:59)

## 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 | 8 | 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
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 | 5 | homer_26.AGATAASR::hsc_lincorr_baso:: homer_18.SAGATAAGRV::hsc_lincorr_baso:: homer_23.BBCTTATCTS::hsc_lincorr_baso:: homer_13.YCTTATCTBN::hsc_lincorr_baso:: homer_14.NBWGATAAGR::hsc_lincorr_baso:: | hsc_lincorr_baso::5_motifs | Show matrix
|  | cluster_2 | 16 | homer_10.MACAGGAAGT::hsc_lincorr_baso:: homer_1.ATTTCCTGTN::hsc_lincorr_baso:: homer_24.VACAGGAAAT::hsc_lincorr_baso:: homer_16.AVCCGGAAGT::hsc_lincorr_baso:: homer_3.AACCGGAAGT::hsc_lincorr_baso:: homer_5.RACCGGAAGT::hsc_lincorr_baso:: homer_11.ACTTCCKGKT::hsc_lincorr_baso:: homer_28.AVCAGGAAGT::hsc_lincorr_baso:: homer_12.ACVAGGAAGT::hsc_lincorr_baso:: homer_17.ANCAGGAAGT::hsc_lincorr_baso:: homer_7.NNAYTTCCTGHN::hsc_lincorr_baso:: homer_6.AGAGGAAGTG::hsc_lincorr_baso:: homer_4.ACAGGAAGTG::hsc_lincorr_baso:: homer_8.ACAGGAAGTG::hsc_lincorr_baso:: homer_2.ACCGGAAGTG::hsc_lincorr_baso:: homer_9.NRYTTCCGGH::hsc_lincorr_baso:: | hsc_lincorr_baso::16_motifs | Show matrix
|  | cluster_3 | 3 | homer_27.YGGCCCCGCCCC::hsc_lincorr_baso:: homer_25.RGKGGGCGKGGC::hsc_lincorr_baso:: homer_29.RGKGGGCGGAGC::hsc_lincorr_baso:: | hsc_lincorr_baso::3_motifs | Show matrix
|  | cluster_4 | 3 | homer_30.AWWWTGCTGAGTCAT::hsc_lincorr_baso:: homer_19.TGCTGAGTCA::hsc_lincorr_baso:: homer_32.VTGACTCATC::hsc_lincorr_baso:: | hsc_lincorr_baso::3_motifs | Show matrix
|  | cluster_5 | 2 | homer_15.TGGCAGTTGG::hsc_lincorr_baso:: homer_21.GGCVGTTR::hsc_lincorr_baso:: | hsc_lincorr_baso::2_motifs | Show matrix
|  | cluster_6 | 1 | homer_31.CAAAGGTCAG::hsc_lincorr_baso | hsc_lincorr_baso : 1 motif | Show matrix
|  | cluster_7 | 1 | homer_20.GCTATTTTTAGC::hsc_lincorr_baso | hsc_lincorr_baso : 1 motif | Show matrix
|  | cluster_8 | 1 | homer_22.CYTGGCABNSTGCCAR::hsc_lincorr_baso | hsc_lincorr_baso : 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
cluster_5
cluster_6
cluster_7
cluster_8
Display Logo Trees
cluster_1
cluster_2
cluster_3
cluster_4
cluster_5
cluster_6
cluster_7
cluster_8
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | -s W G A T A A G r v |  |  | hsc_lincorr_baso::2_motifs | PSSM | 8.91 | 201
Node 2 | v s w G A T A A G r- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 7.17 | 200
Node 3 | v s w G A T A A G r v |  |  | hsc_lincorr_baso::4_motifs | PSSM | 7.93 | 401
Node 4 | v s w G A T A A g r v |  |  | hsc_lincorr_baso::5_motifs | PSSM | 7.50 | 500

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | a a C m G G A A G t-- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 6.36 | 201
Node 2 | a m s m G G A A G t-- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 7.11 | 201
Node 3 | a a C M G G A A G t-- |  |  | hsc_lincorr_baso::3_motifs | PSSM | 6.70 | 302
Node 4 | m a C A G G A A R T-- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 9.55 | 202
Node 5 | A c v A G G A A G T-- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 8.69 | 201
Node 6 | -r C A G G A A G T g- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 8.81 | 201
Node 7 | A c s m G G A A G T-- |  |  | hsc_lincorr_baso::4_motifs | PSSM | 7.75 | 401
Node 8 | -r c c G G A A r y g- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 4.76 | 202
Node 9 | m a C A G G A A r T-- |  |  | hsc_lincorr_baso::3_motifs | PSSM | 9.29 | 301
Node 10 | a m c m G G A A G T-- |  |  | hsc_lincorr_baso::7_motifs | PSSM | 7.00 | 701
Node 11 | -r C m G G A A r y g- |  |  | hsc_lincorr_baso::4_motifs | PSSM | 6.26 | 402
Node 12 | a a c m G G A A r T-- |  |  | hsc_lincorr_baso::10_motifs | PSSM | 7.26 | 1001
Node 13 | -r s m G G A A G t g- |  |  | hsc_lincorr_baso::5_motifs | PSSM | 6.62 | 502
Node 14 | v r s m G G A A g t g s |  |  | hsc_lincorr_baso::6_motifs | PSSM | 6.48 | 602
Node 15 | a a c m G G A A r T g s |  |  | hsc_lincorr_baso::16_motifs | PSSM | 7.04 | 1602

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | r G k G G G C G K r G c-- |  |  | hsc_lincorr_baso::2_motifs | PSSM | 9.08 | 201
Node 2 | r G k G G G C G G r g C y r |  |  | hsc_lincorr_baso::3_motifs | PSSM | 9.51 | 300

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | ----t g m T G A s T C A b |  |  | hsc_lincorr_baso::2_motifs | PSSM | 9.24 | 200
Node 2 | w w w w T G m T G A s T C A t |  |  | hsc_lincorr_baso::3_motifs | PSSM | 9.67 | 300

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | t G r C v G T T r g |  |  | hsc_lincorr_baso::2_motifs | PSSM | 8.00 | 201

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | C A A A G G T C A G |  |  | hsc_lincorr_baso : 1 motif | PSSM | 8.29 | 101

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | G C T A T T T T T A G C |  |  | hsc_lincorr_baso : 1 motif | PSSM | 8.59 | 101

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | C Y T G G C A B N S T G C C A R |  |  | hsc_lincorr_baso : 1 motif | PSSM | 9.50 | 101

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
hsc_lincorr_baso_m23_homer_23.BBCTTATCTS | homer_23.BBCTTATCTS | cluster_1 | hsc_lincorr_baso | 11 | 8.78 | 101 | +S W G A T A A G R R | y y C T T A T C W s+ |  |
hsc_lincorr_baso_m26_homer_26.AGATAASR | homer_26.AGATAASR | cluster_1 | hsc_lincorr_baso | 11 | 6.29 | 101 | ++Y S T T A T C W+ | +w G A T A A s r++ |  |
hsc_lincorr_baso_m27_homer_27.YGGCCCCGCCCC | homer_27.YGGCCCCGCCCC | cluster_3 | hsc_lincorr_baso | 14 | 9.50 | 100 | ++G G G G C G G G R C Y R | y r G y C C C G C C C c++ |  |
hsc_lincorr_baso_m11_homer_11.ACTTCCKGKT | homer_11.ACTTCCKGKT | cluster_2 | hsc_lincorr_baso | 12 | 6.59 | 101 | A A S M G G A A G T++ | ++a C T T C C k s t t |  |
hsc_lincorr_baso_m19_homer_19.TGCTGAGTCA | homer_19.TGCTGAGTCA | cluster_4 | hsc_lincorr_baso | 15 | 9.89 | 100 | ++++t G C T G A s T C A+ | +T G A S T C A G C A++++ |  |
hsc_lincorr_baso_m4_homer_4.ACAGGAAGTG | homer_4.ACAGGAAGTG | cluster_2 | hsc_lincorr_baso | 12 | 9.14 | 100 | +r C M G G A A G T g+ | +C A C T T C C K G Y+ |  |
hsc_lincorr_baso_m17_homer_17.ANCAGGAAGT | homer_17.ANCAGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 8.99 | 100 | A m v A G G A A G T++ | ++A C T T C C T B K T |  |
hsc_lincorr_baso_m25_homer_25.RGKGGGCGKGGC | homer_25.RGKGGGCGKGGC | cluster_3 | hsc_lincorr_baso | 14 | 8.72 | 101 | r G k G G G c G k G g c++ | ++G C C M C G C C C M C Y |  |
hsc_lincorr_baso_m29_homer_29.RGKGGGCGGAGC | homer_29.RGKGGGCGGAGC | cluster_3 | hsc_lincorr_baso | 14 | 10.35 | 100 | r G k G G G C G G r G C++ | ++G C Y C C G C C C M C Y |  |
hsc_lincorr_baso_m28_homer_28.AVCAGGAAGT | homer_28.AVCAGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 8.05 | 100 | a c v m G G A A R t++ | ++A Y T T C C K B G T |  |
hsc_lincorr_baso_m8_homer_8.ACAGGAAGTG | homer_8.ACAGGAAGTG | cluster_2 | hsc_lincorr_baso | 12 | 8.80 | 101 | +a C A G G A A r y r+ | +Y R Y T T C C T G T+ |  |
hsc_lincorr_baso_m16_homer_16.AVCCGGAAGT | homer_16.AVCCGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 7.73 | 101 | A C T T C C G G B T++ | ++a v C C G G A A G t |  |
hsc_lincorr_baso_m24_homer_24.VACAGGAAAT | homer_24.VACAGGAAAT | cluster_2 | hsc_lincorr_baso | 12 | 9.84 | 101 | a a C A G G A A r Y++ | ++R Y T T C C T G T T |  |
hsc_lincorr_baso_m15_homer_15.TGGCAGTTGG | homer_15.TGGCAGTTGG | cluster_5 | hsc_lincorr_baso | 10 | 7.93 | 101 | t G r C a G T T r g | C Y A A C T G Y C A |  |
hsc_lincorr_baso_m9_homer_9.NRYTTCCGGH | homer_9.NRYTTCCGGH | cluster_2 | hsc_lincorr_baso | 12 | 4.12 | 101 | +R S M G G A A R Y G+ | +c r y t T C C k s y+ |  |
hsc_lincorr_baso_m12_homer_12.ACVAGGAAGT | homer_12.ACVAGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 8.80 | 101 | A y v m G G A A G T++ | ++A C T T C C K B R T |  |
hsc_lincorr_baso_m2_homer_2.ACCGGAAGTG | homer_2.ACCGGAAGTG | cluster_2 | hsc_lincorr_baso | 12 | 5.73 | 101 | +r C C G G A A G y g+ | +C R C T T C C G G Y+ |  |
hsc_lincorr_baso_m10_homer_10.MACAGGAAGT | homer_10.MACAGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 9.84 | 100 | R Y T T C C T G T K++ | ++m A C A G G A A R Y |  |
hsc_lincorr_baso_m21_homer_21.GGCVGTTR | homer_21.GGCVGTTR | cluster_5 | hsc_lincorr_baso | 10 | 7.90 | 100 | +G g C v G T T r+ | +Y A A C B G C C+ |  |
hsc_lincorr_baso_m22_homer_22.CYTGGCABNSTGCCAR | homer_22.CYTGGCABNSTGCCAR | cluster_8 | hsc_lincorr_baso | 16 | 9.50 | 101 | c y T G G C w s w s w G C C A r | Y T G G C W S W S W G C C A R G |  |
hsc_lincorr_baso_m6_homer_6.AGAGGAAGTG | homer_6.AGAGGAAGTG | cluster_2 | hsc_lincorr_baso | 12 | 10.48 | 100 | +a G A G G A A G T G+ | +C A C T T C C T C T+ |  |
hsc_lincorr_baso_m5_homer_5.RACCGGAAGT | homer_5.RACCGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 5.90 | 101 | a r C m G G A A G t++ | ++A C T T C C K G Y T |  |
hsc_lincorr_baso_m3_homer_3.AACCGGAAGT | homer_3.AACCGGAAGT | cluster_2 | hsc_lincorr_baso | 12 | 6.92 | 101 | a a C m G G A A G t++ | ++A C T T C C K G T T |  |
hsc_lincorr_baso_m18_homer_18.SAGATAAGRV | homer_18.SAGATAAGRV | cluster_1 | hsc_lincorr_baso | 11 | 9.06 | 100 | +s W G A T A A G r v | B Y C T T A T C W S+ |  |
hsc_lincorr_baso_m7_homer_7.NNAYTTCCTGHN | homer_7.NNAYTTCCTGHN | cluster_2 | hsc_lincorr_baso | 12 | 6.22 | 101 | V R C M G G A W R Y R S | s y r y W T C C k g y b |  |
hsc_lincorr_baso_m14_homer_14.NBWGATAAGR | homer_14.NBWGATAAGR | cluster_1 | hsc_lincorr_baso | 11 | 7.48 | 100 | v s w G A T A A s r+ | +Y S T T A T C W S B |  |
hsc_lincorr_baso_m20_homer_20.GCTATTTTTAGC | homer_20.GCTATTTTTAGC | cluster_7 | hsc_lincorr_baso | 12 | 8.59 | 101 | k C T A T T T w T r G c | G C Y A W A A A T A G M |  |
hsc_lincorr_baso_m13_homer_13.YCTTATCTBN | homer_13.YCTTATCTBN | cluster_1 | hsc_lincorr_baso | 11 | 7.07 | 101 | V S W G A T A A G R+ | +y C T T A T C w s b |  |
hsc_lincorr_baso_m31_homer_31.CAAAGGTCAG | homer_31.CAAAGGTCAG | cluster_6 | hsc_lincorr_baso | 10 | 8.29 | 101 | C m R A G G t C A s | S T G A C C T Y K G |  |
hsc_lincorr_baso_m1_homer_1.ATTTCCTGTN | homer_1.ATTTCCTGTN | cluster_2 | hsc_lincorr_baso | 12 | 9.66 | 101 | S R C A G G A A A T++ | ++A T T T C C T G y s |  |
hsc_lincorr_baso_m32_homer_32.VTGACTCATC | homer_32.VTGACTCATC | cluster_4 | hsc_lincorr_baso | 15 | 8.59 | 101 | +++++G M T G A S T C A B | v T G A s T C A k c+++++ |  |
hsc_lincorr_baso_m30_homer_30.AWWWTGCTGAGTCAT | homer_30.AWWWTGCTGAGTCAT | cluster_4 | hsc_lincorr_baso | 15 | 9.87 | 101 | A T G A C T C A G C A W W W W | w w w w T G C T G A G T C 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