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.

If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

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

Query Motifs

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Name 

Preview 

Matches 

List 

STRGGTCAN
GTAGGTCAC
21 MA0066.1 (PPARG),  MA0072.1 (RORA_2),  MA0258.1 (ESR2),  MA0160.1 (NR4A2),  MA0071.1 (RORA_1),  MA0112.2 (ESR1),  MA0065.2 (PPARG::RXRA),  MA0112.1 (ESR1),  MA0451.1 (kni),  MA0286.1 (CST6)

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2009.meme 476 21

Matches to Query: STRGGTCAN

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Summary 

Alignment 

Name MA0066.1
Alt. Name PPARG
Database JASPAR_CORE_2009.meme
p-value 1.18265e-15
E-value 5.62942e-13
q-value 1.11371e-12
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0072.1
Alt. Name RORA_2
Database JASPAR_CORE_2009.meme
p-value 5.18406e-06
E-value 0.00246761
q-value 0.00162729
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0258.1
Alt. Name ESR2
Database JASPAR_CORE_2009.meme
p-value 8.2576e-05
E-value 0.0393062
q-value 0.0194406
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0160.1
Alt. Name NR4A2
Database JASPAR_CORE_2009.meme
p-value 0.000201059
E-value 0.0957039
q-value 0.0378677
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0071.1
Alt. Name RORA_1
Database JASPAR_CORE_2009.meme
p-value 0.000340104
E-value 0.16189
q-value 0.0533799
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0112.2
Alt. Name ESR1
Database JASPAR_CORE_2009.meme
p-value 0.000556058
E-value 0.264684
q-value 0.0748064
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0065.2
Alt. Name PPARG::RXRA
Database JASPAR_CORE_2009.meme
p-value 0.000710789
E-value 0.338336
q-value 0.0761383
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0112.1
Alt. Name ESR1
Database JASPAR_CORE_2009.meme
p-value 0.000727661
E-value 0.346367
q-value 0.0761383
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0451.1
Alt. Name kni
Database JASPAR_CORE_2009.meme
p-value 0.000997566
E-value 0.474842
q-value 0.0939417
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0286.1
Alt. Name CST6
Database JASPAR_CORE_2009.meme
p-value 0.00283792
E-value 1.35085
q-value 0.205576
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0129.1
Alt. Name TGA1A
Database JASPAR_CORE_2009.meme
p-value 0.00348262
E-value 1.65773
q-value 0.234258
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0159.1
Alt. Name RXR::RAR_DR5
Database JASPAR_CORE_2009.meme
p-value 0.00454754
E-value 2.16463
q-value 0.285497
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MA0141.1
Alt. Name Esrrb
Database JASPAR_CORE_2009.meme
p-value 0.00613294
E-value 2.91928
q-value 0.360965
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0150.1
Alt. Name NFE2L2
Database JASPAR_CORE_2009.meme
p-value 0.00656919
E-value 3.12693
q-value 0.363898
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0018.1
Alt. Name CREB1
Database JASPAR_CORE_2009.meme
p-value 0.00811975
E-value 3.865
q-value 0.414034
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0016.1
Alt. Name usp
Database JASPAR_CORE_2009.meme
p-value 0.00835359
E-value 3.97631
q-value 0.414034
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0074.1
Alt. Name RXRA::VDR
Database JASPAR_CORE_2009.meme
p-value 0.0111267
E-value 5.29629
q-value 0.498956
Overlap 7
Offset -2
Orientation Normal
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Summary 

Alignment 

Name MA0099.1
Alt. Name Fos
Database JASPAR_CORE_2009.meme
p-value 0.0153241
E-value 7.29427
q-value 0.646621
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0272.1
Alt. Name ARG81
Database JASPAR_CORE_2009.meme
p-value 0.0159952
E-value 7.61372
q-value 0.646621
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0099.2
Alt. Name AP1
Database JASPAR_CORE_2009.meme
p-value 0.0164795
E-value 7.84425
q-value 0.646621
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0434.1
Alt. Name YPR013C
Database JASPAR_CORE_2009.meme
p-value 0.0189633
E-value 9.02652
q-value 0.686842
Overlap 8
Offset 1
Orientation Normal
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TOMTOM version
4.8.0 (Release date: Wed Jan 11 15:32:51 EST 2012)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):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 5.765 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.