TOol for Motif TO Motif comparison (TOMTOM)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

Query Motifs  |  Target Databases  |  Matches  |  Program information  |  Explanation

Query Motifs

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Name 

Alt. Name 

Preview 

Matches 

List 

AGRKGGC 1.2e-2727
AGGGGGC
3 MA0139.1 (CTCF) , Sp4_primary, MA0155.1 (INSM1)
CCACYAG 5.5e-290
CCACTAG
1 MA0139.1 (CTCF)
RGAAA 2.3e-183
AGAAA
0
GTGGHCA 5.5e-136
GTGGCCA
1 MA0147.1 (Myc)
CGCCNCC 2.8e-109
CGCCTCC
1 Sp4_primary
AAYTRCA 6.3e-061
AACTGCA
0
AGRKGGA 1.9e-058
AGAGGGA
0
TTTAWW 1.0e-050
TTTAAT
0
DCCACM 1.8e-043
GCCACA
0
RGGAA 9.6e-035
AGGAA
2 MA0144.1 (Stat3) , MA0080.2 (SPI1)
DAAATR 7.3e-023
AAAATG
0
GTAYTRC 4.3e-022
GTACTGC
0
AHACAMA 8.6e-018
ACACACA
0
AGCGHCC 2.3e-017
AGCGCCC
0
AGCAGAG 9.8e-016
AGCAGAG
0
GTGTCRC 7.1e-016
GTGTCAC
0
RTTCTS 3.6e-010
GTTCTG
0
GTGGTDA 1.7e-008
GTGGTGA
0
GRACAC 2.3e-006
GGACAC
0
CASCATC 2.1e-005
CAGCATC
0
GATGTCA 1.8e-004
GATGTCA
0
ATGWACA 4.4e-004
ATGAACA
0
CTGYCTC 1.2e-003
CTGCCTC
0
GGAAGTS 1.1e-003
GGAAGTG
5 MA0062.2 (GABPA) , MA0080.2 (SPI1) , Gabpa_primary, MA0076.1 (ELK4) , MA0062.1 (GABPA)
CTGYAG 2.1e-003
CTGCAG
0
CTGGYCA 1.4e-002
CTGGCCA
0
GTTTTM 3.7e-002
GTTTTA
0
GAGGACA 4.3e-002
GAGGACA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

jaspar_vertebrates.meme 146 8
uniprobe_mouse.meme 386 2

Matches to Query: AGRKGGC (1.2e-2727)

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Summary 

Alignment 

Name MA0139.1
Alt. Name CTCF
Database jaspar_vertebrates.meme
p-value 1.03468e-09
E-value 5.50452e-07
q-value 1.09396e-06
Overlap 7
Offset 8
Orientation Normal
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Summary 

Alignment 

Name Sp4_primary
Database uniprobe_mouse.meme
p-value 3.31533e-05
E-value 0.0176375
q-value 0.0175263
Overlap 7
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0155.1
Alt. Name INSM1
Database jaspar_vertebrates.meme
p-value 7.98759e-05
E-value 0.042494
q-value 0.0281506
Overlap 7
Offset 4
Orientation Normal
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Matches to Query: CCACYAG (5.5e-290)

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Summary 

Alignment 

Name MA0139.1
Alt. Name CTCF
Database jaspar_vertebrates.meme
p-value 5.76231e-06
E-value 0.00306555
q-value 0.0061311
Overlap 7
Offset 3
Orientation Normal
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Matches to Query: RGAAA (2.3e-183)

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Matches to Query: GTGGHCA (5.5e-136)

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Summary 

Alignment 

Name MA0147.1
Alt. Name Myc
Database jaspar_vertebrates.meme
p-value 1.83358e-05
E-value 0.00975463
q-value 0.0194046
Overlap 5
Offset 5
Orientation Normal
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Matches to Query: CGCCNCC (2.8e-109)

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Summary 

Alignment 

Name Sp4_primary
Database uniprobe_mouse.meme
p-value 7.34237e-05
E-value 0.0390614
q-value 0.0456843
Overlap 7
Offset 5
Orientation Normal
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Matches to Query: AAYTRCA (6.3e-061)

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Matches to Query: AGRKGGA (1.9e-058)

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Matches to Query: TTTAWW (1.0e-050)

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Matches to Query: DCCACM (1.8e-043)

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Matches to Query: RGGAA (9.6e-035)

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Summary 

Alignment 

Name MA0144.1
Alt. Name Stat3
Database jaspar_vertebrates.meme
p-value 3.57577e-05
E-value 0.0190231
q-value 0.0322883
Overlap 5
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0080.2
Alt. Name SPI1
Database jaspar_vertebrates.meme
p-value 6.12524e-05
E-value 0.0325863
q-value 0.0322883
Overlap 5
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: DAAATR (7.3e-023)

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Matches to Query: GTAYTRC (4.3e-022)

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Matches to Query: AHACAMA (8.6e-018)

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Matches to Query: AGCGHCC (2.3e-017)

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Matches to Query: AGCAGAG (9.8e-016)

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Matches to Query: GTGTCRC (7.1e-016)

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Matches to Query: RTTCTS (3.6e-010)

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Matches to Query: GTGGTDA (1.7e-008)

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Matches to Query: GRACAC (2.3e-006)

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Matches to Query: CASCATC (2.1e-005)

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Matches to Query: GATGTCA (1.8e-004)

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Matches to Query: ATGWACA (4.4e-004)

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Matches to Query: CTGYCTC (1.2e-003)

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Matches to Query: GGAAGTS (1.1e-003)

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Summary 

Alignment 

Name MA0062.2
Alt. Name GABPA
Database jaspar_vertebrates.meme
p-value 3.01609e-06
E-value 0.00160456
q-value 0.00317372
Overlap 7
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0080.2
Alt. Name SPI1
Database jaspar_vertebrates.meme
p-value 1.16065e-05
E-value 0.00617466
q-value 0.00610653
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name Gabpa_primary
Database uniprobe_mouse.meme
p-value 2.01854e-05
E-value 0.0107386
q-value 0.00708009
Overlap 7
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0076.1
Alt. Name ELK4
Database jaspar_vertebrates.meme
p-value 5.62914e-05
E-value 0.029947
q-value 0.0148083
Overlap 6
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0062.1
Alt. Name GABPA
Database jaspar_vertebrates.meme
p-value 7.4423e-05
E-value 0.039593
q-value 0.0156625
Overlap 7
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: CTGYAG (2.1e-003)

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Matches to Query: CTGGYCA (1.4e-002)

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Matches to Query: GTTTTM (3.7e-002)

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Matches to Query: GAGGACA (4.3e-002)

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TOMTOM version
4.5.0 (Release date: Wed Oct 20 15:18:53 EST 2010)
Reference
Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble, "Quantifying similarity between motifs",
Genome Biology, 8:R24, 2007
Command line summary

Background letter frequencies (from first motif database):
A: 0.250   C: 0.250   G: 0.250   T: 0.250

Result calculation took 12.205 seconds
show model parameters...

Explanation of TOMTOM Results

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The TOMTOM results consist of

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name
The motif name.
Alt. Name
The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website
A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview
The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches
The number of significant matches.
List
Links to the first 20 matches
Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database
The database name.
Number of Motifs
The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched
The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name
The name of the matched motif.
Alt. Name
The alternative name of the matched motif.
p-value
The probability that the match occurred by random chance according to the null model.
E-value
The expected number of false positives in the matches up to this point.
q-value
The minimum False Discovery Rate required to include the match.
Overlap
The number of letters that overlaped in the optimal alignment.
Offset
The offset of the query motif to the matched motif in the optimal alignment.
Orientation
The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.
Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type
Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars
Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC
Toggle adding pseudocounts for Small Sample Correction.
Flip
Toggle a full reverse complement of the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.