TOMTOM

Name	Preview	Matches	List
1_re_1_0.319	GAGAATCGCTTG	0
2_re_15_0.321	GTAATCCCA	1	PITX2_Q2_M00482_T
3_re_5_0.323	ACGCCTGTA	0
4_re_75_0.325	CTCACTGCACCC	1	Zbtb3_primary_SCI09_U
5_re_94_0.332	GGCCTCCCA	0
6_re_37_0.332	CCAAAGTGCTG	0
7_re_26_0.335	CGCTTGAACC	0
8_re_136_0.336	AGGCTGGTC	1	SMAP1L_4_H
9_re_64_0.341	TCGAGACCA	0
10_re_105_0.341	TGGGCAACA	0
11_re_58_0.350	CGGTGGCTC	0
12_re_98_0.350	TAACATGGTG	0
13_re_34_0.355	GATCGCGCC	0
14_re_10_0.356	AATTAGCCG	1	UME6_MA0412.1_J
15_re_53_0.378	ACTCCGTCT	0
16_re_228_0.402	CAGACGTGA	0
17_re_187_0.410	ACCTCAGGT	0
18_h_14_0.568	CGGATTTGCA	7	NMI_8_H, SRBD1_3_H, DGCR8_4_H, FOXM1_7_H, NFIX_2_H, NOC2L_4_H, IL24_5_H
19_e_415_0.541	AGAAGGGTG	0
20_e_309_0.534	CATTTTAC	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	11

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

PITX2_Q2_M00482_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.16326e-06

E-value

0.00923987

q-value

0.0184797

Overlap

Offset

Orientation

Normal

Name

Zbtb3_primary_SCI09_U

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.22821e-05

E-value

0.0358761

q-value

0.0717523

Overlap

Offset

Orientation

Normal

Name

SMAP1L_4_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

7.39568e-06

E-value

0.0216028

q-value

0.0432055

Overlap

Offset

-1

Orientation

Normal

Name

UME6_MA0412.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.86543e-06

E-value

0.00836992

q-value

0.0159841

Overlap

Offset

Orientation

Reverse Complement

Name

NMI_8_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

5.80643e-07

E-value

0.00169606

q-value

0.00337531

Overlap

Offset

-2

Orientation

Reverse Complement

Name

SRBD1_3_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.54651e-06

E-value

0.00743835

q-value

0.00353389

Overlap

Offset

-3

Orientation

Reverse Complement

Name

DGCR8_4_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.359e-06

E-value

0.00981163

q-value

0.00353389

Overlap

Offset

-3

Orientation

Reverse Complement

Name

FOXM1_7_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.64753e-06

E-value

0.0106544

q-value

0.00353389

Overlap

Offset

-4

Orientation

Reverse Complement

Name

NFIX_2_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.64753e-06

E-value

0.0106544

q-value

0.00353389

Overlap

Offset

-4

Orientation

Reverse Complement

Name

NOC2L_4_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.64753e-06

E-value

0.0106544

q-value

0.00353389

Overlap

Offset

-4

Orientation

Reverse Complement

Name

IL24_5_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.10444e-05

E-value

0.0322606

q-value

0.00917167

Overlap

Offset

-2

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_1_0.319

Matches to Query: 2_re_15_0.321

Summary

Alignment

Matches to Query: 3_re_5_0.323

Matches to Query: 4_re_75_0.325

Summary

Alignment

Matches to Query: 5_re_94_0.332

Matches to Query: 6_re_37_0.332

Matches to Query: 7_re_26_0.335

Matches to Query: 8_re_136_0.336

Summary

Alignment

Matches to Query: 9_re_64_0.341

Matches to Query: 10_re_105_0.341

Matches to Query: 11_re_58_0.350

Matches to Query: 12_re_98_0.350

Matches to Query: 13_re_34_0.355

Matches to Query: 14_re_10_0.356

Summary

Alignment

Matches to Query: 15_re_53_0.378

Matches to Query: 16_re_228_0.402

Matches to Query: 17_re_187_0.410

Matches to Query: 18_h_14_0.568

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 19_e_415_0.541

Matches to Query: 20_e_309_0.534

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