# RSAT - matrix-clustering result

### Analysis: oct4_motifs_found_in_chen_2008_peak_sets_discovered_by_peak-motifs,_meme-chip_and_homer (18/05/2026 07:46)

## 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
66 | 3 | 13 | 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
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 | 37 | MEME_ChIP_3::oct4_meme-chip:: positions_8nt_m4::oct4_peak_motifs:: oligos_7nt_mkv5_m4::oct4_peak_motifs:: homer_9::oct4_homer:: positions_7nt_m4::oct4_peak_motifs:: positions_8nt_m3::oct4_peak_motifs:: MEME_ChIP_1::oct4_meme-chip:: MEME_ChIP_15::oct4_meme-chip:: MEME_ChIP_20::oct4_meme-chip:: MEME_ChIP_21::oct4_meme-chip:: MEME_ChIP_24::oct4_meme-chip:: homer_13::oct4_homer:: local_words_7nt_m3::oct4_peak_motifs:: MEME_ChIP_13::oct4_meme-chip:: MEME_ChIP_14::oct4_meme-chip:: oligos_7nt_mkv5_m2::oct4_peak_motifs:: MEME_ChIP_11::oct4_meme-chip:: MEME_ChIP_12::oct4_meme-chip:: MEME_ChIP_17::oct4_meme-chip:: MEME_ChIP_19::oct4_meme-chip:: local_words_8nt_m3::oct4_peak_motifs:: MEME_ChIP_23::oct4_meme-chip:: oligos_7nt_mkv5_m1::oct4_peak_motifs:: MEME_ChIP_16::oct4_meme-chip:: MEME_ChIP_18::oct4_meme-chip:: positions_8nt_m2::oct4_peak_motifs:: positions_7nt_m1::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:: homer_1::oct4_homer:: MEME_ChIP_10::oct4_meme-chip:: MEME_ChIP_25::oct4_meme-chip:: | oct4_peak_motifs::17_motifs oct4_meme-chip::17_motifs oct4_homer::3_motifs | Show matrix
|  | cluster_2 | 7 | homer_19::oct4_homer:: MEME_ChIP_5::oct4_meme-chip:: oligos_8nt_mkv6_m3::oct4_peak_motifs:: oligos_8nt_mkv6_m4::oct4_peak_motifs:: homer_4::oct4_homer:: oligos_8nt_mkv6_m1::oct4_peak_motifs:: oligos_8nt_mkv6_m2::oct4_peak_motifs:: | oct4_meme-chip::1_motif oct4_homer::2_motifs oct4_peak_motifs::4_motifs | Show matrix
|  | cluster_3 | 4 | MEME_ChIP_22::oct4_meme-chip:: homer_6::oct4_homer:: homer_16::oct4_homer:: homer_18::oct4_homer:: | oct4_homer::3_motifs oct4_meme-chip::1_motif | Show matrix
|  | cluster_4 | 5 | oligos_7nt_mkv5_m3::oct4_peak_motifs:: homer_12::oct4_homer:: MEME_ChIP_8::oct4_meme-chip:: MEME_ChIP_2::oct4_meme-chip:: MEME_ChIP_9::oct4_meme-chip:: | oct4_meme-chip::3_motifs oct4_homer::1_motif oct4_peak_motifs::1_motif | Show matrix
|  | cluster_5 | 2 | homer_15::oct4_homer:: homer_3::oct4_homer:: | oct4_homer::2_motifs | Show matrix
|  | cluster_6 | 3 | homer_14::oct4_homer:: MEME_ChIP_4::oct4_meme-chip:: MEME_ChIP_7::oct4_meme-chip:: | oct4_homer::1_motif oct4_meme-chip::2_motifs | Show matrix
|  | cluster_7 | 2 | homer_11::oct4_homer:: homer_2::oct4_homer:: | oct4_homer::2_motifs | Show matrix
|  | cluster_8 | 1 | homer_10::oct4_homer | oct4_homer : 1 motif | Show matrix
|  | cluster_9 | 1 | homer_17::oct4_homer | oct4_homer : 1 motif | Show matrix
|  | cluster_10 | 1 | homer_5::oct4_homer | oct4_homer : 1 motif | Show matrix
|  | cluster_11 | 1 | homer_8::oct4_homer | oct4_homer : 1 motif | Show matrix
|  | cluster_12 | 1 | homer_7::oct4_homer | oct4_homer : 1 motif | Show matrix
|  | cluster_13 | 1 | MEME_ChIP_6::oct4_meme-chip | oct4_meme-chip : 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
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
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 | ---------T A T G c w A A T------ |  |  | oct4_meme-chip::2_motifs | PSSM | 7.61 | 41
Node 6 | ------t w k T A T G C W A A T k a r m-- |  |  | oct4_meme-chip::2_motifs | PSSM | 10.53 | 41
Node 7 | --------w T A T G c w A A T k w---- |  |  | oct4_meme-chip::2_motifs | PSSM | 9.33 | 41
Node 8 | ---------T A T G c w A A T------ |  |  | oct4_meme-chip::3_motifs | PSSM | 8.16 | 62
Node 9 | ---------T A T G C w A A T------ |  |  | oct4_meme-chip::4_motifs | PSSM | 8.61 | 82
Node 10 | ---y w T T s w y A T G C A a A t------ |  |  | oct4_meme-chip::2_motifs | PSSM | 10.18 | 1502
Node 11 | --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 12 | ---y w T T s w t A T G C A a A t------ |  |  | oct4_meme-chip::2_motifs oct4_homer::1_motif | PSSM | 8.12 | 5122
Node 13 | --------w w A T G C A A A T g w---- |  |  | oct4_peak_motifs::1_motif oct4_meme-chip::2_motifs | PSSM | 7.64 | 1094
Node 14 | -------a w T A T G c w A A T t----- |  |  | oct4_meme-chip::2_motifs | PSSM | 8.40 | 41
Node 15 | -------a w T A T G C w A A T t w g--- |  |  | oct4_meme-chip::2_motifs | PSSM | 10.28 | 41
Node 16 | --------w y A T G C A A A T k m r--- |  |  | oct4_peak_motifs::1_motif oct4_meme-chip::3_motifs | PSSM | 9.30 | 3381
Node 17 | ------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
Node 18 | -------a w w A T G C T A A t t----- |  |  | oct4_meme-chip::2_motifs oct4_peak_motifs::1_motif | PSSM | 6.55 | 1541
Node 19 | --------w y A T G C A A A T k h r--- |  |  | oct4_peak_motifs::2_motifs oct4_meme-chip::3_motifs | PSSM | 8.61 | 4325
Node 20 | ------g c a T A T G C G C A T A t r c-- |  |  | oct4_peak_motifs::2_motifs oct4_homer::1_motif | PSSM | 8.31 | 880
Node 21 | ------t s A T A T G C A A A T g w r m-- |  |  | oct4_peak_motifs::1_motif oct4_meme-chip::2_motifs | PSSM | 7.74 | 1124
Node 22 | -------a w y A T G C A A A T k h r--- |  |  | oct4_meme-chip::5_motifs oct4_peak_motifs::2_motifs | PSSM | 8.84 | 4365
Node 23 | -------a w t A T G C A A A T k h r--- |  |  | oct4_peak_motifs::3_motifs oct4_meme-chip::7_motifs | PSSM | 7.74 | 5906
Node 24 | --s y w T T g w t A T G C A a A t k w m--- |  |  | oct4_homer::1_motif oct4_meme-chip::2_motifs oct4_peak_motifs::6_motifs | PSSM | 8.68 | 9547
Node 25 | ---------T A T G Y w A A T------ |  |  | oct4_meme-chip::5_motifs | PSSM | 9.91 | 1938
Node 26 | 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 27 | ------t c w t A T G C A A A T k h r m-- |  |  | oct4_peak_motifs::4_motifs oct4_meme-chip::9_motifs | PSSM | 7.63 | 7029
Node 28 | --y y a T T G T y A T G y w--------- |  |  | oct4_peak_motifs::2_motifs | PSSM | 7.31 | 1333
Node 29 | ------t c w t A T G C A A A T k m r m-- |  |  | oct4_peak_motifs::4_motifs oct4_homer::1_motif oct4_meme-chip::9_motifs | PSSM | 7.58 | 9084
Node 30 | ------t c w t A T G C A A A T k m r m-- |  |  | oct4_meme-chip::14_motifs oct4_homer::1_motif oct4_peak_motifs::4_motifs | PSSM | 7.82 | 11021
Node 31 | --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::7_motifs oct4_meme-chip::2_motifs oct4_homer::1_motif | PSSM | 8.99 | 9738
Node 32 | --y y w T T G T y A T G y w--------- |  |  | oct4_peak_motifs::2_motifs oct4_meme-chip::1_motif | PSSM | 7.95 | 2085
Node 33 | w y c y w T T s w t A T G C A a A t k w a t r m |  |  | oct4_meme-chip::2_motifs oct4_homer::1_motif oct4_peak_motifs::9_motifs | PSSM | 8.70 | 10528
Node 34 | w y c y w T T s w t A T G C A A A T k w r t r m |  |  | oct4_homer::2_motifs oct4_meme-chip::16_motifs oct4_peak_motifs::13_motifs | PSSM | 9.15 | 21548
Node 35 | w y c y w T T s w t A T G C A a A T k w r y r m |  |  | oct4_meme-chip::16_motifs oct4_homer::3_motifs oct4_peak_motifs::15_motifs | PSSM | 8.76 | 22427
Node 36 | w y c y w T T g w t A T G C A a A T k w r y r m |  |  | oct4_peak_motifs::17_motifs oct4_meme-chip::17_motifs oct4_homer::3_motifs | PSSM | 8.85 | 24506

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | y g C G C m T G C G c r-- |  |  | oct4_peak_motifs::2_motifs | PSSM | 7.51 | 1815
Node 2 | y g C G C m T G C G c r s k |  |  | oct4_peak_motifs::2_motifs oct4_homer::1_motif | PSSM | 7.69 | 2334
Node 3 | --C G C A T G C G C A-- |  |  | oct4_homer::1_motif oct4_meme-chip::1_motif | PSSM | 11.02 | 896
Node 4 | y g C G S m T G C G c v s k |  |  | oct4_homer::1_motif oct4_peak_motifs::3_motifs | PSSM | 7.07 | 3215
Node 5 | b g C G C m T G C G c v s k |  |  | oct4_homer::1_motif oct4_peak_motifs::4_motifs | PSSM | 6.47 | 3889
Node 6 | b g C G C m T G C G c r s k |  |  | oct4_meme-chip::1_motif oct4_homer::2_motifs oct4_peak_motifs::4_motifs | PSSM | 6.90 | 4785

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | ------y T k k k t T t T k---- |  |  | oct4_homer::2_motifs | PSSM | 5.08 | 4327
Node 2 | --T T T G y T k k k t T t T k---- |  |  | oct4_homer::3_motifs | PSSM | 8.35 | 4597
Node 3 | m K T T T G y T k k k t T t T k w w k G |  |  | oct4_homer::3_motifs oct4_meme-chip::1_motif | PSSM | 11.23 | 4624

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | C C M C d C C C C C m |  |  | oct4_meme-chip::2_motifs | PSSM | 11.13 | 1356
Node 2 | C C C C d C C c C C m |  |  | oct4_meme-chip::3_motifs | PSSM | 11.66 | 2070
Node 3 | Y y y y y y Y y C y m |  |  | oct4_meme-chip::3_motifs oct4_homer::1_motif | PSSM | 7.26 | 11911
Node 4 | y y Y y y y C y C y s |  |  | oct4_meme-chip::3_motifs oct4_homer::1_motif oct4_peak_motifs::1_motif | PSSM | 5.72 | 13592

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | s C w G C T G C T G C y b s |  |  | oct4_homer::2_motifs | PSSM | 8.10 | 12091

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | y T T C C t G--- |  |  | oct4_meme-chip::2_motifs | PSSM | 7.14 | 8886
Node 2 | y T y C C w G s a r |  |  | oct4_homer::1_motif oct4_meme-chip::2_motifs | PSSM | 4.10 | 16399

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | a G g s w r r s C W G g r r |  |  | oct4_homer::2_motifs | PSSM | 6.12 | 15043

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | C C T G K C T C T G |  |  | oct4_homer : 1 motif | PSSM | 5.38 | 10526

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T G T G T G T G T G |  |  | oct4_homer : 1 motif | PSSM | 4.37 | 256

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | R G G G G C G G G G C C K G |  |  | oct4_homer : 1 motif | PSSM | 12.64 | 480

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | K K A G G T G T G G C C T T |  |  | oct4_homer : 1 motif | PSSM | 7.99 | 154

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T C C C A G C A C C C A C A |  |  | oct4_homer : 1 motif | PSSM | 11.18 | 184

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | C A A G G T C A |  |  | oct4_meme-chip : 1 motif | PSSM | 10.56 | 236

- 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_meme-chip_m1_MEME_ChIP_1 | MEME_ChIP_1 | cluster_1 | oct4_meme-chip | 24 | 8.47 | 1856 | ++++++++++T T W R C A T+++++++ | +++++++A T G Y w A A++++++++++ |  |
oct4_homer_m8_homer_8 | homer_8 | cluster_11 | oct4_homer | 14 | 7.99 | 154 | k k r G g T G T G g y c y t | A R G R C C A C A C C Y M M |  |
oct4_meme-chip_m22_MEME_ChIP_22 | MEME_ChIP_22 | cluster_3 | oct4_meme-chip | 20 | 12.60 | 27 | C M W W M W A A A M A M A R M A A M M K | m K k T T k y T k T k T t t w k w w k G |  |
oct4_peak_motifs_m2_oligos_7nt_mkv5_m2 | oligos_7nt_mkv5_m2 | cluster_1 | oct4_peak_motifs | 24 | 6.43 | 1500 | ++++++++w w A T G C T A A t t+++++ | +++++A A T T A G C A T W W++++++++ |  |
oct4_meme-chip_m25_MEME_ChIP_25 | MEME_ChIP_25 | cluster_1 | oct4_meme-chip | 24 | 9.96 | 135 | +++Y W T T S W T A T G C W A A T++++++ | ++++++a T t w G C A T a w s A A w r+++ |  |
oct4_homer_m2_homer_2 | homer_2 | cluster_7 | oct4_homer | 14 | 7.46 | 5787 | a G g C w G G s C T k G r r | Y Y C M A G S C C W G C C T |  |
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_homer_m15_homer_15 | homer_15 | cluster_5 | oct4_homer | 14 | 6.46 | 4947 | S C W G C W G C W G++++ | ++++C w G C w G C w G s |  |
oct4_peak_motifs_m15_oligos_8nt_mkv6_m4 | oligos_8nt_mkv6_m4 | cluster_2 | oct4_peak_motifs | 14 | 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_meme-chip_m4_MEME_ChIP_4 | MEME_ChIP_4 | cluster_6 | oct4_meme-chip | 10 | 6.59 | 5320 | Y T T C C Y++++ | ++++r G G A A r |  |
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_meme-chip_m5_MEME_ChIP_5 | MEME_ChIP_5 | cluster_2 | oct4_meme-chip | 14 | 9.76 | 307 | ++++Y M T G C G C A++ | ++T G C G C A k r++++ |  |
oct4_meme-chip_m18_MEME_ChIP_18 | MEME_ChIP_18 | cluster_1 | oct4_meme-chip | 24 | 10.32 | 21 | ++++++++w T A T G c w A A T k w++++ | ++++W M A T T W G C A T A W++++++++ |  |
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_homer_m7_homer_7 | homer_7 | cluster_12 | oct4_homer | 14 | 11.18 | 184 | k C C C A g C a C C C A C a | T G T G G G T G C T G G G M |  |
oct4_homer_m6_homer_6 | homer_6 | cluster_3 | oct4_homer | 20 | 9.98 | 270 | ++C A A A A C A A A A C A A A++++ | ++++T T T G T T t T G t T t T G++ |  |
oct4_meme-chip_m19_MEME_ChIP_19 | MEME_ChIP_19 | cluster_1 | oct4_meme-chip | 24 | 10.70 | 20 | +++++++a w T A T G C w A A T k A g+++ | +++C T M A T T W G C A T A W T+++++++ |  |
oct4_homer_m5_homer_5 | homer_5 | cluster_10 | oct4_homer | 14 | 12.64 | 480 | r G G G G C G G R G C s k s | S M S G C Y C C G C C C C Y |  |
oct4_peak_motifs_m21_positions_8nt_m3 | positions_8nt_m3 | cluster_1 | oct4_peak_motifs | 24 | 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_homer_m13_homer_13 | homer_13 | cluster_1 | oct4_homer | 24 | 7.74 | 2056 | ++++++++++W T G C W A A T K M++++ | ++++k m A T t W G C A 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_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_meme-chip_m12_MEME_ChIP_12 | MEME_ChIP_12 | cluster_1 | oct4_meme-chip | 24 | 9.00 | 21 | +++++++a w T A T G C w A A T k+++++ | +++++M A T T W G C A T A W T+++++++ |  |
oct4_meme-chip_m2_MEME_ChIP_2 | MEME_ChIP_2 | cluster_4 | oct4_meme-chip | 11 | 9.38 | 1298 | C C M C d C C C+++ | +++G G G H G K G G |  |
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_m14_oligos_8nt_mkv6_m3 | oligos_8nt_mkv6_m3 | cluster_2 | oct4_peak_motifs | 14 | 7.34 | 674 | s s C G C T T C C G s s++ | ++S S C G G A A G C G S S |  |
oct4_peak_motifs_m13_oligos_8nt_mkv6_m2 | oligos_8nt_mkv6_m2 | cluster_2 | oct4_peak_motifs | 14 | 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_meme-chip_m10_MEME_ChIP_10 | MEME_ChIP_10 | cluster_1 | oct4_meme-chip | 24 | 10.26 | 1367 | +++y w T T s w y A T G C A a A t++++++ | ++++++A T T T G C A T R W S A A W R+++ |  |
oct4_homer_m1_homer_1 | homer_1 | cluster_1 | oct4_homer | 24 | 7.11 | 3620 | +++y w T T s w t A T G c A a A+++++++ | +++++++T T T G C A T A W S A A W R+++ |  |
oct4_homer_m18_homer_18 | homer_18 | cluster_3 | oct4_homer | 20 | 4.44 | 289 | ++++++T T T T T T T T T T++++ | ++++A A A A A A A A A A++++++ |  |
oct4_meme-chip_m7_MEME_ChIP_7 | MEME_ChIP_7 | cluster_6 | oct4_meme-chip | 10 | 6.64 | 3566 | +T Y C C W G+++ | +++C w G G r A+ |  |
oct4_homer_m4_homer_4 | homer_4 | cluster_2 | oct4_homer | 14 | 9.16 | 519 | y G C G C A t G C G C r s k | M S Y G C G C A T G C G C R |  |
oct4_meme-chip_m3_MEME_ChIP_3 | MEME_ChIP_3 | cluster_1 | oct4_meme-chip | 24 | 9.09 | 752 | ++++W T T G T Y A T++++++++++++ | ++++++++++++A T r A C A A w++++ |  |
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_meme-chip_m20_MEME_ChIP_20 | MEME_ChIP_20 | cluster_1 | oct4_meme-chip | 24 | 9.83 | 21 | +++++++++A T T W G C A T A++++++ | ++++++T A T G C w A A T+++++++++ |  |
oct4_meme-chip_m21_MEME_ChIP_21 | MEME_ChIP_21 | cluster_1 | oct4_meme-chip | 24 | 7.67 | 21 | +++++++++T A T G c w A A T++++++ | ++++++A T T W G C A T A+++++++++ |  |
oct4_homer_m11_homer_11 | homer_11 | cluster_7 | oct4_homer | 14 | 4.59 | 9257 | +++S W R R G C W G R G+ | +c y C w G c y y w s+++ |  |
oct4_peak_motifs_m7_local_words_7nt_m3 | local_words_7nt_m3 | cluster_1 | oct4_peak_motifs | 24 | 7.58 | 1083 | ++++++w s A T A T G C A A A T g w++++ | ++++W C A T T T G C A T A T S W++++++ |  |
oct4_meme-chip_m24_MEME_ChIP_24 | MEME_ChIP_24 | cluster_1 | oct4_meme-chip | 24 | 7.71 | 21 | +++++++++T A T G y w A A T++++++ | ++++++A T T W R C A T A+++++++++ |  |
oct4_meme-chip_m6_MEME_ChIP_6 | MEME_ChIP_6 | cluster_13 | oct4_meme-chip | 8 | 10.56 | 236 | C A A G G T C A | T G A C C T T G |  |
oct4_meme-chip_m15_MEME_ChIP_15 | MEME_ChIP_15 | cluster_1 | oct4_meme-chip | 24 | 10.68 | 20 | +++++++++A T T T G C A T A++++++ | ++++++T A T G C A A A T+++++++++ |  |
oct4_meme-chip_m8_MEME_ChIP_8 | MEME_ChIP_8 | cluster_4 | oct4_meme-chip | 11 | 9.34 | 714 | ++C C k C C k C C+ | +G G M G G M G G++ |  |
oct4_meme-chip_m11_MEME_ChIP_11 | MEME_ChIP_11 | cluster_1 | oct4_meme-chip | 24 | 7.82 | 21 | ++++++++w T A T G c w A A T t+++++ | +++++A A T T W G C A T A W++++++++ |  |
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_homer_m9_homer_9 | homer_9 | cluster_1 | oct4_homer | 24 | 11.37 | 148 | ++++++A W A T G C G C A T A Y S M++++ | ++++k s r T A T G C G C A T w t++++++ |  |
oct4_homer_m16_homer_16 | homer_16 | cluster_3 | oct4_homer | 20 | 5.35 | 4038 | ++++++Y T K K K T T T T K++++ | ++++m A a A a m m m A r++++++ |  |
oct4_meme-chip_m17_MEME_ChIP_17 | MEME_ChIP_17 | cluster_1 | oct4_meme-chip | 24 | 10.01 | 21 | +++++++w w T A T G C w A A T t w++++ | ++++W A A T T W G C A T A W W+++++++ |  |
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_homer_m12_homer_12 | homer_12 | cluster_4 | oct4_homer | 11 | 7.15 | 9841 | Y Y Y Y Y Y Y Y Y Y+ | +r R r r r r r r r R |  |
oct4_meme-chip_m13_MEME_ChIP_13 | MEME_ChIP_13 | cluster_1 | oct4_meme-chip | 24 | 10.81 | 21 | ++++++t w k T A T G C W A A T k m r m++ | ++K Y K M A T T W G C A T A M W A++++++ |  |
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_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_meme-chip_m14_MEME_ChIP_14 | MEME_ChIP_14 | cluster_1 | oct4_meme-chip | 24 | 10.37 | 21 | ++++++y w d T A T G C W A A T k a r m++ | ++K Y T M A T T W G C A T A H W R++++++ |  |
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+++ |  |
oct4_homer_m17_homer_17 | homer_17 | cluster_9 | oct4_homer | 10 | 4.37 | 256 | T G T G T G T G T G | C A C A C A C A C A |  |
oct4_meme-chip_m23_MEME_ChIP_23 | MEME_ChIP_23 | cluster_1 | oct4_meme-chip | 24 | 10.48 | 2287 | ++++++++W Y A T G C A A A T K M R+++ | +++y k m A T T T G C A T r w++++++++ |  |
oct4_meme-chip_m16_MEME_ChIP_16 | MEME_ChIP_16 | cluster_1 | oct4_meme-chip | 24 | 8.60 | 21 | ++++++++w T A T G y w A A T k w++++ | ++++W M A T T W R C A T A W++++++++ |  |
oct4_meme-chip_m9_MEME_ChIP_9 | MEME_ChIP_9 | cluster_4 | oct4_meme-chip | 11 | 10.41 | 58 | C C C C w C C y C C m | K G G R G G W G G G G |  |
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_m12_oligos_8nt_mkv6_m1 | oligos_8nt_mkv6_m1 | cluster_2 | oct4_peak_motifs | 14 | 7.44 | 1056 | S S C G C C T G C G C S++ | ++s g C G C A G G C G s s |  |
oct4_peak_motifs_m11_positions_7nt_m4 | positions_7nt_m4 | cluster_1 | oct4_peak_motifs | 24 | 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_homer_m14_homer_14 | homer_14 | cluster_6 | oct4_homer | 10 | 2.84 | 7519 | Y T S C W G R R A R | y t y y C w g s a r |  |
oct4_homer_m19_homer_19 | homer_19 | cluster_2 | oct4_homer | 14 | 11.03 | 589 | ++C G C A T G C G C A++ | ++T G C G C A T G C G++ |  |
oct4_peak_motifs_m3_oligos_7nt_mkv5_m3 | oligos_7nt_mkv5_m3 | cluster_4 | oct4_peak_motifs | 11 | 6.53 | 1681 | S S G A G G G C G S S | s s C G C C C T C s s |  |
oct4_homer_m3_homer_3 | homer_3 | cluster_5 | oct4_homer | 14 | 9.09 | 7145 | s C t s C T G C T g C y b s | S V R G C A G C A G S A G S |  |
oct4_homer_m10_homer_10 | homer_10 | cluster_8 | oct4_homer | 10 | 5.38 | 10526 | s C W k k s t y W g | C W R A S M M W G S |  |
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

Cluster composition by collection
Collections Overlap

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.
Collections Complementarity | A dynamic heatmap showing how many motifs contribute each collection to each 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