TOMTOM

Name	Preview	Matches	List
1_e_k4me3_2_0.786	CCGCCGCCG	2	ERF2_01_M01057_T, ADF1_Q6_M00171_T
2_h_k4me3_3_0.731	AAACGCGA	0
3_h_k4me3_2_0.719	CAATTCCG	2	STAT1_02_M00492_T, STAT1_01_M00224_T
4_e_k4me3_7_0.707	CGCAGGCGC	2	ZFP206_01_M01742_T, TRIM69_7_H
5_e_k4me3_48_0.692	CGCCGCTTC	0
6_h_k4me3_4_0.685	TAAACGTT	0
7_e_k4me3_61_0.684	CGGCGCCCA	0
8_e_k4me3_45_0.655	AAGATGGCG	1	REX1_03_M01744_T
9_e_k4me3_250_0.648	CTACGGAA	0
10_e_k27ac_29_0.369	AGCTGCCTG	0
11_e_k27ac_226_0.379	CACAAAGGG	1	SOX10_MA0442.1_J
12_h_k9me3_15_0.390	GAGCATGCATGC	0
13_e_k4me1_412_0.402	AGCAGACAC	0
14_e_k4me3_210_0.598	CACGCTCT	0
15_e_k36me3_245_0.404	GGCCAGCAC	0
16_e_k36me3_303_0.411	ACCTTGGCC	0
17_e_k36me3_361_0.423	CATGTCCAC	0
18_h_k27ac_10_0.428	TCATTCAGAG	0
19_h_k27me3_23_0.558	GGTTATTT	1	HMEF2_Q6_M00406_T
20_h_k36me3_6_0.462	CAGCAGCAGCAG	2	MYF_01_M01302_T, Myf_MA0055.1_J

Name

Preview

Matches

List

1_e_k4me3_2_0.786

CCGCCGCCG

ERF2_01_M01057_T, ADF1_Q6_M00171_T

STAT1_02_M00492_T, STAT1_01_M00224_T

4_e_k4me3_7_0.707

CGCAGGCGC

ZFP206_01_M01742_T, TRIM69_7_H

15_e_k36me3_245_0.404

GGCCAGCAC

16_e_k36me3_303_0.411

ACCTTGGCC

17_e_k36me3_361_0.423

MYF_01_M01302_T, Myf_MA0055.1_J

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	11

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

ERF2_01_M01057_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.7749e-06

E-value

0.00518447

q-value

0.0103087

Overlap

Offset

-1

Orientation

Normal

Name

ADF1_Q6_M00171_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.1719e-05

E-value

0.0342311

q-value

0.0340321

Overlap

Offset

Orientation

Normal

Name

STAT1_02_M00492_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

4.51167e-06

E-value

0.0131786

q-value

0.0259727

Overlap

Offset

Orientation

Normal

Name

STAT1_01_M00224_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.50445e-05

E-value

0.0439449

q-value

0.0433039

Overlap

Offset

Orientation

Normal

Name

ZFP206_01_M01742_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

4.27293e-07

E-value

0.00124812

q-value

0.00249075

Overlap

Offset

Orientation

Normal

Name

TRIM69_7_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.16283e-06

E-value

0.00339664

q-value

0.00338916

Overlap

Offset

Orientation

Normal

Name

REX1_03_M01744_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

8.8463e-06

E-value

0.0258401

q-value

0.0516801

Overlap

Offset

Orientation

Normal

Name

SOX10_MA0442.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

9.77166e-07

E-value

0.0028543

q-value

0.00570861

Overlap

Offset

-1

Orientation

Reverse Complement

Name

HMEF2_Q6_M00406_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

4.43005e-06

E-value

0.0129402

q-value

0.0258769

Overlap

Offset

Orientation

Reverse Complement

Name

MYF_01_M01302_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.29967e-06

E-value

0.00379634

q-value

0.00379634

Overlap

Offset

Orientation

Normal

Name

Myf_MA0055.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.29967e-06

E-value

0.00379634

q-value

0.00379634

Overlap

Offset

Orientation

Normal

The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

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.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: 1_e_k4me3_2_0.786

Summary

Alignment

Summary

Alignment

Matches to Query: 2_h_k4me3_3_0.731

Matches to Query: 3_h_k4me3_2_0.719

Summary

Alignment

Summary

Alignment

Matches to Query: 4_e_k4me3_7_0.707

Summary

Alignment

Summary

Alignment

Matches to Query: 5_e_k4me3_48_0.692

Matches to Query: 6_h_k4me3_4_0.685

Matches to Query: 7_e_k4me3_61_0.684

Matches to Query: 8_e_k4me3_45_0.655

Summary

Alignment

Matches to Query: 9_e_k4me3_250_0.648

Matches to Query: 10_e_k27ac_29_0.369

Matches to Query: 11_e_k27ac_226_0.379

Summary

Alignment

Matches to Query: 12_h_k9me3_15_0.390

Matches to Query: 13_e_k4me1_412_0.402

Matches to Query: 14_e_k4me3_210_0.598

Matches to Query: 15_e_k36me3_245_0.404

Matches to Query: 16_e_k36me3_303_0.411

Matches to Query: 17_e_k36me3_361_0.423

Matches to Query: 18_h_k27ac_10_0.428

Matches to Query: 19_h_k27me3_23_0.558

Summary

Alignment

Matches to Query: 20_h_k36me3_6_0.462

Summary

Alignment

Summary

Alignment

TOMTOM version

Reference

Command line summary

Model parameters

Explanation of TOMTOM Results

The TOMTOM results consist of

Inputs

Query Motifs

Target Databases

Matches

Summary Table

Alignment

Create custom LOGO