# RSAT - matrix-clustering result

### Analysis: arac2 (20/01/2026 14:33)

## 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
28 | 1 | 21 | Download | Download |
average | Ncor | Ncor = 0.55 cor = 0.7

| 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
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 | 4 | GSIYRPFYSK_HTCS_Rgu-2::Collection_1:: GTVYKPFYSK_HTCS_Rgu-2::Collection_1:: GTVYRPFYSK_HTCS_Rgu-2::Collection_1:: GTVYKPYYSK_HTCS_Rgu-2::Collection_1:: | Collection_1::4_motifs | Show matrix
|  | cluster_2 | 2 | SVQYRPSYAK_HTCS_Fru::Collection_1:: SVQYRPSYTK_HTCS_Fru::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_3 | 2 | SSLNKPKYAR_HTCS_Ara-1::Collection_1:: SSLNKPKYTR_HTCS_Ara-1::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_4 | 2 | PRTHRSNHST_RhaS::Collection_1:: PRTNRSNYSS_RhaS::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_5 | 2 | SSNHLSSYAT_HTCS_Hep::Collection_1:: SSNHLPSYAT_HTCS_Hep::Collection_1:: | Collection_1::2_motifs | Show matrix
|  | cluster_6 | 1 | SSRSHQLYSR_AraC::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_7 | 1 | SSRAHQLYSR_AraC::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_8 | 1 | GVQYRPSYTR_HTCS_Fru::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_9 | 1 | SSVFKPRYSK_HTCS_Rgu-1::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_10 | 1 | SSTYRTGYRQ_HTCS_Ara-2::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_11 | 1 | SSTYRSVYRQ_HTCS_Ara-2::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_12 | 1 | ATNFTSRYSK_HTCS_Hya::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_13 | 1 | SRQYRRGTYK_HTCS_Man-2::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_14 | 1 | SRSYRKVTFK_HTCS_Man-1_3::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_15 | 1 | SSWRKTEHFS_RhaR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_16 | 1 | SASYTISYST_HTCS_Ogl-2::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_17 | 1 | SSSYRPKYAT_HTCS_Aga-1::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_18 | 1 | SRVRQSNYSV_RhaR::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_19 | 1 | SSTYRTVYRQ_HTCS_Ara-2::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_20 | 1 | SKQYRHSYSK_HTCS_Pga::Collection_1 | Collection_1 : 1 motif | Show matrix
|  | cluster_21 | 1 | SYHHRTSYIT_AdaA::Collection_1 | Collection_1 : 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
cluster_18
cluster_19
cluster_20
cluster_21
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
Display Branch-Motifs
cluster_1

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | T r g A m w A w w w T m C A w w w w w w T G k A w w w T w k T c y A |  |  | Collection_1::2_motifs | PSSM | 17.89 | 50
Node 2 | T r g A m w A w w w T m C A w w w w w w T G k A w w w T w k T c y A |  |  | Collection_1::3_motifs | PSSM | 17.33 | 66
Node 3 | T r g A m w A w w d T m C A w w w w w w T G k A h w w T w k T c y A |  |  | Collection_1::4_motifs | PSSM | 17.11 | 78

cluster_2

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | g w w W s w W w y w w w w w w w w w w w w r w W w s W w w c |  |  | Collection_1::2_motifs | PSSM | 12.15 | 38

cluster_3

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w G k y s r m C m w w h r a r y t y d w w k G k y s r m C w |  |  | Collection_1::2_motifs | PSSM | 16.01 | 24

cluster_4

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | A y C T T c r y m w t w y T G C C A n n n n n n n n n n n n n n n T G G C A r w a w k r y g A A G r T |  |  | Collection_1::2_motifs | PSSM | 24.86 | 28

cluster_5

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Node 1 | w y A A W T t T r w w w w w w w w w w w w w y A a A W T T r w |  |  | Collection_1::2_motifs | PSSM | 14.33 | 20

cluster_6

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | T a d s r a w w k w w y c s m T A w w w w T A k s g r m w m w w t y s h t R |  |  | Collection_1 : 1 motif | PSSM | 13.57 | 39

cluster_7

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | h d r s r k d w a w d T r s m T R w w w w Y A k s y A h w t w h m y s y h d |  |  | Collection_1 : 1 motif | PSSM | 16.66 | 16

cluster_8

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | r m A w s w w d m n n n n n n n n n n n n k h w w s w T k y |  |  | Collection_1 : 1 motif | PSSM | 13.95 | 4

cluster_9

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | s w r w A a w T w y w v w w w w w w w w w b w r w A w t T w y w s |  |  | Collection_1 : 1 motif | PSSM | 12.16 | 52

cluster_10

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w r A w y r w t y w w w w w w w w w w w w w r a w y r w T y w |  |  | Collection_1 : 1 motif | PSSM | 11.44 | 12

cluster_11

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w b w w h d w k h w w w w w w w w w w w w w w d m w h d w w v w |  |  | Collection_1 : 1 motif | PSSM | 19.41 | 4

cluster_12

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w G w A y w r T w y w w w w w w w w w w w w r w A y w r T w C w |  |  | Collection_1 : 1 motif | PSSM | 13.26 | 24

cluster_13

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | d k w C r h w w w h d b r d m w n n n n n w k h y v h d w w w d y G w m h |  |  | Collection_1 : 1 motif | PSSM | 20.19 | 4

cluster_14

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | k k r y r c w d w h r T k h m m n n n n n k k d m A y d w h w g y r y m m |  |  | Collection_1 : 1 motif | PSSM | 13.37 | 16

cluster_15

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y C A A A T C a a a a a a a a a a a a a a T C A A A A a |  |  | Collection_1 : 1 motif | PSSM | 22.39 | 5

cluster_16

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | d T T m r h r m w T h w y k m w w w w w w w w k m r w d A w k y d y k A A h |  |  | Collection_1 : 1 motif | PSSM | 29.99 | 4

cluster_17

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | y k r T m w w y w T T y r w w w w w w w w y r A A w r w w k A y m r |  |  | Collection_1 : 1 motif | PSSM | 16.97 | 6

cluster_18

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w T C T T G A A A A A w m G A C s d d d d d d d d d d d d d d d d d C G T y r A A A A T T T A A G G T |  |  | Collection_1 : 1 motif | PSSM | 48.21 | 3

cluster_19

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w r m w m k w k y w n n n n n n n n n n n n w r m w m k w k y w |  |  | Collection_1 : 1 motif | PSSM | 13.86 | 4

cluster_20

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w y m G w y y k r w y w T w n n n n n n n w A w r w y m r r w C k r w |  |  | Collection_1 : 1 motif | PSSM | 22.18 | 4

cluster_21

## Branch Motifs
Node | Consensus | Logo | Logo (Reverse) | Collections | Matrix (Transfac format) | IC | Nb sites
--- | --- | --- | --- | --- | --- | --- | ---
Singleton | w k y r w k A T m w y r m w A T |  |  | Collection_1 : 1 motif | PSSM | 13.86 | 2

- 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)
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
Collection_1_m16_SSLNKPKYTR_HTCS_Ara-1 | SSLNKPKYTR_HTCS_Ara-1 | cluster_3 | Collection_1 | 30 | 15.85 | 22 | w G k y s r m C m w w h r a r y t y d w w k G k y s r m C w | W G K Y S R M C M W W H R A R Y T Y D W W K G K Y S R M C W |  |
Collection_1_m24_GTVYKPFYSK_HTCS_Rgu-2 | GTVYKPFYSK_HTCS_Rgu-2 | cluster_1 | Collection_1 | 34 | 18.38 | 16 | T R G A V W A W T K T H C A W W W W W W T G D A M A W T W B T C Y A | T r g A v W A w T k T h C A w w w w w w T G d A m A w T W b T c y A |  |
Collection_1_m14_SSRAHQLYSR_AraC | SSRAHQLYSR_AraC | cluster_7 | Collection_1 | 38 | 16.66 | 16 | h d r s r k d w a w d T r s m T R w w w w Y A k s y A h w t w h m y s y h d | H D R S R K D W A W D T R S M T R W W W W Y A K S Y A H W T W H M Y S Y H D |  |
Collection_1_m18_GTVYRPFYSK_HTCS_Rgu-2 | GTVYRPFYSK_HTCS_Rgu-2 | cluster_1 | Collection_1 | 34 | 19.61 | 32 | T r g A m d A w t w T m C A w w w w w w T G k A w a w T h k T c y A | T R G A M D A W T W T M C A W W W W W W T G K A W A W T H K T C Y A |  |
Collection_1_m7_ATNFTSRYSK_HTCS_Hya | ATNFTSRYSK_HTCS_Hya | cluster_12 | Collection_1 | 32 | 13.26 | 24 | w G w A y w r T w y w w w w w w w w w w w w r w A y w r T w C w | W G W A Y W R T W Y W W W W W W W W W W W W R W A Y W R T W C W |  |
Collection_1_m23_SRVRQSNYSV_RhaR | SRVRQSNYSV_RhaR | cluster_18 | Collection_1 | 51 | 48.21 | 3 | w T C T T G A A A A A w m G A C s d d d d d d d d d d d d d d d d d C G T y r A A A A T T T A A G G T | A C C T T A A A T T T T Y R A C G H H H H H H H H H H H H H H H H H S G T C K W T T T T T C A A G A W |  |
Collection_1_m26_SSVFKPRYSK_HTCS_Rgu-1 | SSVFKPRYSK_HTCS_Rgu-1 | cluster_9 | Collection_1 | 33 | 12.16 | 52 | s w r w A a w T w y w v w w w w w w w w w b w r w A w t T w y w s | S W R W A A W T W Y W V W W W W W W W W W B W R W A W T T W Y W S |  |
Collection_1_m15_SSTYRTVYRQ_HTCS_Ara-2 | SSTYRTVYRQ_HTCS_Ara-2 | cluster_19 | Collection_1 | 32 | 13.86 | 4 | w r m w m k w k y w n n n n n n n n n n n n w r m w m k w k y w | W R M W M K W K Y W N N N N N N N N N N N N W R M W M K W K Y W |  |
Collection_1_m8_GVQYRPSYTR_HTCS_Fru | GVQYRPSYTR_HTCS_Fru | cluster_8 | Collection_1 | 30 | 13.95 | 4 | R M A w s w W d m n n n n n n n n n n n n k h W w s w T K Y | R M A W S W W D M N N N N N N N N N N N N K H W W S W T K Y |  |
Collection_1_m9_SSSYRPKYAT_HTCS_Aga-1 | SSSYRPKYAT_HTCS_Aga-1 | cluster_17 | Collection_1 | 34 | 16.97 | 6 | y k r T m w w y w T T y r w w w w w w w w y r A A w r w w k A y m r | Y K R T M W W Y W T T Y R W W W W W W W W Y R A A W R W W K A Y M R |  |
Collection_1_m2_GSIYRPFYSK_HTCS_Rgu-2 | GSIYRPFYSK_HTCS_Rgu-2 | cluster_1 | Collection_1 | 34 | 20.78 | 12 | T R K A B W A W W R T M C A W W W W W W T G K A Y W W T W V T M Y A | T r k A b w A w w r T m C A w w w w w w T G k A y w w T w v T m y A |  |
Collection_1_m21_SRSYRKVTFK_HTCS_Man-1_3 | SRSYRKVTFK_HTCS_Man-1_3 | cluster_14 | Collection_1 | 37 | 13.37 | 16 | k k r y r c w d w h r T k h m m n n n n n k k d m A y d w h w g y r y m m | K K R Y R C W D W H R T K H M M N N N N N K K D M A Y D W H W G Y R Y M M |  |
Collection_1_m17_SYHHRTSYIT_AdaA | SYHHRTSYIT_AdaA | cluster_21 | Collection_1 | 16 | 13.86 | 2 | w k y r w k A T m w y r m w A T | A T W K Y R W K A T M W Y R M W |  |
Collection_1_m13_SSLNKPKYAR_HTCS_Ara-1 | SSLNKPKYAR_HTCS_Ara-1 | cluster_3 | Collection_1 | 30 | 24.95 | 2 | w G k y s r m C w m A w r w r y w y w T k w G k y s r m C w | W G K Y S R M C W M A W R W R Y W Y W T K W G K Y S R M C W |  |
Collection_1_m3_SSTYRSVYRQ_HTCS_Ara-2 | SSTYRSVYRQ_HTCS_Ara-2 | cluster_11 | Collection_1 | 32 | 19.41 | 4 | w b w w h d w k h w w w w w w w w w w w w w w d m w h d w w v w | W B W W H D W K H W W W W W W W W W W W W W W D M W H D W W V W |  |
Collection_1_m5_SSWRKTEHFS_RhaR | SSWRKTEHFS_RhaR | cluster_15 | Collection_1 | 28 | 22.39 | 5 | y C A A A T C a a a a a a a a a a a a a a T C A A A A a | T T T T T G A T T T T T T T T T T T T T T G A T T T G R |  |
Collection_1_m20_SVQYRPSYTK_HTCS_Fru | SVQYRPSYTK_HTCS_Fru | cluster_2 | Collection_1 | 30 | 13.06 | 26 | g w w W s w W w y w w w w w w w w w w w w r w W w s W w w c | G W W W S W W W Y W W W W W W W W W W W W R W W W S W W W C |  |
Collection_1_m4_GTVYKPYYSK_HTCS_Rgu-2 | GTVYKPYYSK_HTCS_Rgu-2 | cluster_1 | Collection_1 | 34 | 17.27 | 18 | T r r A m w A w w k T m C A w w w w w w T G k A m w w T w k T y y A | T R R A M W A W W K T M C A W W W W W W T G K A M W W T W K T Y Y A |  |
Collection_1_m12_SSRSHQLYSR_AraC | SSRSHQLYSR_AraC | cluster_6 | Collection_1 | 38 | 13.57 | 39 | T a d s r a w w k w w y c s m T A w w w w T A k s g r m w m w w t y s h t R | Y A D S R A W W K W K Y C S M T A W W W W T A K S G R W W M W W T Y S H T A |  |
Collection_1_m25_SKQYRHSYSK_HTCS_Pga | SKQYRHSYSK_HTCS_Pga | cluster_20 | Collection_1 | 35 | 22.18 | 4 | w y m G w y y k r w y w T w n n n n n n n w A w r w y m r r w C k r w | W Y M G W Y Y K R W Y W T W N N N N N N N W A W R W Y M R R W C K R W |  |
Collection_1_m1_SSNHLSSYAT_HTCS_Hep | SSNHLSSYAT_HTCS_Hep | cluster_5 | Collection_1 | 31 | 17.36 | 8 | w C M W A T w T r d w w w w w w w w w w w h y A w A T W K G w | W C M W A T W T R D W W W W W W W W W W W H Y A W A T W K G W |  |
Collection_1_m11_SRQYRRGTYK_HTCS_Man-2 | SRQYRRGTYK_HTCS_Man-2 | cluster_13 | Collection_1 | 37 | 20.19 | 4 | d k W C R h w w w h d b R d m w n n n n n w k h Y v h d w w w d Y G W m h | D K W C R H W W W H D B R D M W N N N N N W K H Y V H D W W W D Y G W M H |  |
Collection_1_m19_PRTHRSNHST_RhaS | PRTHRSNHST_RhaS | cluster_4 | Collection_1 | 51 | 26.92 | 20 | A C C T T Y v y m h t w y T G C C A n n n n n n n n n n n n n n n T G G C A r w a d k r b R A A G G T | A C C T T Y V Y M H T W Y T G C C A N N N N N N N N N N N N N N N T G G C A R W A D K R B R A A G G T |  |
Collection_1_m6_SSNHLPSYAT_HTCS_Hep | SSNHLPSYAT_HTCS_Hep | cluster_5 | Collection_1 | 31 | 15.99 | 12 | w y a A w w T T r w w w w w w w w w w w w w y A A w w T t r w | W Y A A W W T T R W W W W W W W W W W W W W Y A A W W T T R W |  |
Collection_1_m10_SVQYRPSYAK_HTCS_Fru | SVQYRPSYAK_HTCS_Fru | cluster_2 | Collection_1 | 30 | 11.13 | 12 | r w w w s w W w y w w w w w w w w w w w w r w W w s w w w y | R W W W S W W W Y W W W W W W W W W W W W R W W W S W W W Y |  |
Collection_1_m22_SASYTISYST_HTCS_Ogl-2 | SASYTISYST_HTCS_Ogl-2 | cluster_16 | Collection_1 | 38 | 29.99 | 4 | d T T m R h r M W T h w Y k M W w w w w w w W K m R w d A W K y d Y k A A h | D T T M R H R M W T H W Y K M W W W W W W W W K M R W D A W K Y D Y K A A H |  |
Collection_1_m28_SSTYRTGYRQ_HTCS_Ara-2 | SSTYRTGYRQ_HTCS_Ara-2 | cluster_10 | Collection_1 | 31 | 11.44 | 12 | w r A w y r w t y w w w w w w w w w w w w w r a w y r w T y w | W R A W Y R W T Y W W W W W W W W W W W W W R A W Y R W T Y W |  |
Collection_1_m27_PRTNRSNYSS_RhaS | PRTNRSNYSS_RhaS | cluster_4 | Collection_1 | 51 | 27.67 | 8 | w y C T T s r k h w h w m T G C C A n n n n n n n n n n n n n n n T G G C A k w d w d m y s A A G r w | W Y C T T S R K H W H W M T G C C A N N N N N N N N N N N N N N N T G G C A K W D W D M Y S A A G R 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