TOMTOM

Name	Preview	Matches	List
1_e_0_0.722	CTGTAATCCCAGC	1	PITX2_Q2_M00482_T
2_e_10_0.689	ATCACTTGAA	0
3_e_28_0.684	GCCTCCCAA	1	IK_Q5_M01169_T
4_e_21_0.682	CAGCCTCCCG	0
5_e_13_0.681	GTCTCGAAC	1	RPC155_01_M01798_T
6_e_40_0.677	CTGGGCAACA	0
7_e_24_0.667	TCTCGAACTC	1	RPC155_01_M01798_T
8_e_18_0.661	AAATTAGCCG	1	IVD_4_H
9_e_57_0.658	ACTTTGGGA	1	LUN1_01_M00480_T
10_e_5_0.652	AGCTACTCGG	0
11_e_56_0.650	AGGGTTTCAC	0
12_e_35_0.646	GCCACTGCA	0
13_e_27_0.633	AGAGACGGGG	0
14_e_20_0.631	GGCAGATCA	0
15_e_7_0.628	AGATCGCGC	0
16_e_22_0.625	GACGGAGTC	0
17_e_201_0.616	AAAATACGA	0
18_e_89_0.588	CAGGTGATCT	1	sna_MA0086.1_J
19_e_135_0.585	AAGTAGCTG	1	LUN1_01_M00480_T
20_e_232_0.544	ATAACGACG	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	6

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

PITX2_Q2_M00482_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.22738e-06

E-value

0.00650617

q-value

0.0130123

Overlap

Offset

-1

Orientation

Normal

Name

IK_Q5_M01169_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.07321e-06

E-value

0.00605584

q-value

0.0121117

Overlap

Offset

Orientation

Reverse Complement

Name

RPC155_01_M01798_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.63936e-06

E-value

0.0106306

q-value

0.0212612

Overlap

Offset

Orientation

Reverse Complement

Name

RPC155_01_M01798_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.53097e-08

E-value

0.00010314

q-value

0.000206279

Overlap

Offset

Orientation

Reverse Complement

Name

IVD_4_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.34069e-05

E-value

0.0391615

q-value

0.0769819

Overlap

Offset

-1

Orientation

Normal

Name

LUN1_01_M00480_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.98106e-08

E-value

8.70766e-05

q-value

0.000174153

Overlap

Offset

Orientation

Normal

Name

sna_MA0086.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.67261e-06

E-value

0.0048857

q-value

0.00953727

Overlap

Offset

Orientation

Normal

Name

LUN1_01_M00480_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

3.56248e-07

E-value

0.0010406

q-value

0.00207949

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_e_0_0.722

Summary

Alignment

Matches to Query: 2_e_10_0.689

Matches to Query: 3_e_28_0.684

Summary

Alignment

Matches to Query: 4_e_21_0.682

Matches to Query: 5_e_13_0.681

Summary

Alignment

Matches to Query: 6_e_40_0.677

Matches to Query: 7_e_24_0.667

Summary

Alignment

Matches to Query: 8_e_18_0.661

Summary

Alignment

Matches to Query: 9_e_57_0.658

Summary

Alignment

Matches to Query: 10_e_5_0.652

Matches to Query: 11_e_56_0.650

Matches to Query: 12_e_35_0.646

Matches to Query: 13_e_27_0.633

Matches to Query: 14_e_20_0.631

Matches to Query: 15_e_7_0.628

Matches to Query: 16_e_22_0.625

Matches to Query: 17_e_201_0.616

Matches to Query: 18_e_89_0.588

Summary

Alignment

Matches to Query: 19_e_135_0.585

Summary

Alignment

Matches to Query: 20_e_232_0.544

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