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 

h120-k4me1-29_re_221_0.437
TGTGACGTCATC
19 JDP2_dimeric_3_P,  JDP2_dimeric_1_P,  Jdp2_dimeric_1_P,  CREB3_dimeric_0_P,  Creb5_dimeric_0_P,  Atf1_primary_SCI09_U,  XBP1_dimeric_0_P,  STF1_02_M01187_T,  TGA2_01_M01586_T,  Jundm2_primary_SCI09_U
npc20-k27ac-31_re_254_0.433
ACCTCATC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiTaipaleCmbned.meme 3764 19

Matches to Query: h120-k4me1-29_re_221_0.437

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Summary 

Alignment 

Name JDP2_dimeric_3_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 7.32302e-08
E-value 0.000275638
q-value 0.000330722
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name JDP2_dimeric_1_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.10088e-07
E-value 0.000414371
q-value 0.000330722
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Jdp2_dimeric_1_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.33967e-07
E-value 0.000504251
q-value 0.000330722
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name CREB3_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.44764e-07
E-value 0.00129769
q-value 0.000638336
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name Creb5_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.16877e-07
E-value 0.00194553
q-value 0.000765605
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Atf1_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 9.26593e-07
E-value 0.0034877
q-value 0.00104059
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name XBP1_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.07527e-06
E-value 0.00404732
q-value 0.00104059
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name STF1_02_M01187_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.16319e-06
E-value 0.00437825
q-value 0.00104059
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name TGA2_01_M01586_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.47794e-06
E-value 0.00556298
q-value 0.00104059
Overlap 12
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Jundm2_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.53991e-06
E-value 0.00579622
q-value 0.00104059
Overlap 12
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name ATF3_Q6_M00513_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.74239e-06
E-value 0.00655835
q-value 0.00104059
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name ATF7_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.88511e-06
E-value 0.00709557
q-value 0.00104059
Overlap 12
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name STF1_01_M01186_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.49151e-06
E-value 0.00937805
q-value 0.0011568
Overlap 12
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name CREB_Q4_M00178_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.86436e-06
E-value 0.0145455
q-value 0.00168351
Overlap 12
Offset 0
Orientation Normal
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Summary 

Alignment 

Name VJUN_01_M00036_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 8.32086e-06
E-value 0.0313197
q-value 0.00308124
Overlap 12
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name BATF3_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 9.53269e-06
E-value 0.035881
q-value 0.00322251
Overlap 12
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name ATF_B_M00338_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 9.57258e-06
E-value 0.0360312
q-value 0.00322251
Overlap 11
Offset -1
Orientation Normal
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Summary 

Alignment 

Name CREB1_MA0018.2_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.63856e-05
E-value 0.0616752
q-value 0.00433401
Overlap 8
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name CREB_Q2_01_M00916_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.59593e-05
E-value 0.0977109
q-value 0.00620182
Overlap 12
Offset 0
Orientation Normal
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Matches to Query: npc20-k27ac-31_re_254_0.433

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TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 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: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 8.704 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.