TOMTOM

Name	Preview	Matches	List
1_re_126_0.800	CGCGGCGCC	2	STP1_01_M01685_T, ODC1_3_H
2_h_5_0.750	ACGCGAAA	5	SWI4_MA0401.1_J, E2F_Q6_M00427_T, E2F1_Q6_M00431_T, E2F_Q4_M00426_T, E2F_Q3_M00425_T
3_h_7_0.731	TTCGGTACCG	0
4_e_20_0.720	CGGAGCCCG	0
5_re_93_0.291	CAGGCTGGA	0
6_re_100_0.291	CTCCTGACCA	0
7_re_84_0.312	CCAAAGTGC	0
8_re_132_0.327	AGTGCTGGG	1	ZNF503_4_H
9_e_76_0.670	CACAGCGACG	0
10_e_52_0.667	AGCTCGCGC	0
11_e_285_0.666	AAATAACGTA	0
12_re_146_0.337	CCTGGGTGA	0
13_re_161_0.339	CACCTGTAG	0
14_re_144_0.349	ACCCCATCT	0
15_re_134_0.355	ACATGCCA	0
16_re_29_0.357	ACTCTGTCT	0
17_h_25_0.627	TTTAAAGG	0
18_e_215_0.617	CAATCACCG	0
19_e_120_0.575	AGTCCCGCC	1	SP2_01_M01783_T
20_e_112_0.571	CCGTTTCCCT	1	VSX1_11_H

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	10

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

STP1_01_M01685_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.34038e-05

E-value

0.0391525

q-value

0.0401769

Overlap

Offset

Orientation

Normal

Name

ODC1_3_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.37991e-05

E-value

0.0403072

q-value

0.0401769

Overlap

Offset

-1

Orientation

Normal

Name

SWI4_MA0401.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.86475e-06

E-value

0.00836795

q-value

0.0167359

Overlap

Offset

Orientation

Normal

Name

E2F_Q6_M00427_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

7.73739e-06

E-value

0.0226009

q-value

0.0191491

Overlap

Offset

Orientation

Reverse Complement

Name

E2F1_Q6_M00431_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.41679e-05

E-value

0.0413844

q-value

0.0191491

Overlap

Offset

Orientation

Reverse Complement

Name

E2F_Q4_M00426_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.41679e-05

E-value

0.0413844

q-value

0.0191491

Overlap

Offset

Orientation

Reverse Complement

Name

E2F_Q3_M00425_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.63892e-05

E-value

0.0478728

q-value

0.0191491

Overlap

Offset

Orientation

Reverse Complement

Name

ZNF503_4_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

9.39858e-06

E-value

0.0274532

q-value

0.0549065

Overlap

Offset

-1

Orientation

Normal

Name

SP2_01_M01783_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.54939e-06

E-value

0.0103678

q-value

0.0207355

Overlap

Offset

-1

Orientation

Reverse Complement

Name

VSX1_11_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

9.55527e-06

E-value

0.0279109

q-value

0.0555934

Overlap

Offset

Orientation

Reverse Complement

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_re_126_0.800

Summary

Alignment

Summary

Alignment

Matches to Query: 2_h_5_0.750

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 3_h_7_0.731

Matches to Query: 4_e_20_0.720

Matches to Query: 5_re_93_0.291

Matches to Query: 6_re_100_0.291

Matches to Query: 7_re_84_0.312

Matches to Query: 8_re_132_0.327

Summary

Alignment

Matches to Query: 9_e_76_0.670

Matches to Query: 10_e_52_0.667

Matches to Query: 11_e_285_0.666

Matches to Query: 12_re_146_0.337

Matches to Query: 13_re_161_0.339

Matches to Query: 14_re_144_0.349

Matches to Query: 15_re_134_0.355

Matches to Query: 16_re_29_0.357

Matches to Query: 17_h_25_0.627

Matches to Query: 18_e_215_0.617

Matches to Query: 19_e_120_0.575

Summary

Alignment

Matches to Query: 20_e_112_0.571

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