TOMTOM

Name	Preview	Matches	List
1_h_k27me3-npc_0.582	CCCGCAGGTGAG	2	sna_MA0086.1_J, RAV1_02_M00344_T
2_h_k27me3-npc_0.575	ATACCTGCCG	0
3_h_k27me3-npc_0.571	TTTCCCTCGA	0
4_h_k27me3-npc_0.570	GGGAGAAAGC	0
5_e_k27me3-npc_0.565	GAAGAAATC	0
6_e_k27me3-npc_0.560	CAGAACCCA	0
7_e_k27me3-h1_0.556	AAGGTCACA	2	NR4A2_MA0160.1_J, GTF3C5_2_H
8_e_k27me3-h1_0.553	TCATGCATT	0
9_e_k27me3-h1_0.549	ACACTGTGA	0
10_h_k27me3-h1_0.545	GTGTGTGTGT	0
11_h_k27me3-h1_0.545	CACAGAATGTTT	0
12_e_k27me3-npc_0.544	GATGCTGGA	0
13_e_k27me3-h1_0.544	GACTTAAAA	0
14_h_k27me3-npc_0.542	AGGTCGGTCC	0
15_e_k27me3-npc_0.540	CCGCTATTC	0
16_e_k27me3-npc_0.540	ACTTGTTCT	0
17_e_k27me3-h1_0.540	AGCCCACGA	0
18_e_k27me3-h1_0.538	CTTGACCTC	0
19_e_k27me3-npc_0.537	ATCGATAAA	1	DAL80_01_M01619_T
20_e_k27me3-h1_0.526	GGTACTTAG	0

Name

Preview

Matches

List

1_h_k27me3-npc_0.582

CCCGCAGGTGAG

sna_MA0086.1_J, RAV1_02_M00344_T

NR4A2_MA0160.1_J, GTF3C5_2_H

12_e_k27me3-npc_0.544

GATGCTGGA

13_e_k27me3-h1_0.544

GACTTAAAA

14_h_k27me3-npc_0.542

AGGTCGGTCC

15_e_k27me3-npc_0.540

CCGCTATTC

16_e_k27me3-npc_0.540

19_e_k27me3-npc_0.537

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	5

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

sna_MA0086.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

4.97371e-06

E-value

0.0145282

q-value

0.0147554

Overlap

Offset

-4

Orientation

Normal

Name

RAV1_02_M00344_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

5.1321e-06

E-value

0.0149909

q-value

0.0147554

Overlap

Offset

Orientation

Reverse Complement

Name

NR4A2_MA0160.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.31392e-06

E-value

0.00383796

q-value

0.00621805

Overlap

Offset

Orientation

Normal

Name

GTF3C5_2_H

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.14601e-06

E-value

0.00626851

q-value

0.00621805

Overlap

Offset

-2

Orientation

Reverse Complement

Name

DAL80_01_M01619_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.25285e-05

E-value

0.0365957

q-value

0.0731914

Overlap

Offset

-2

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_h_k27me3-npc_0.582

Summary

Alignment

Summary

Alignment

Matches to Query: 2_h_k27me3-npc_0.575

Matches to Query: 3_h_k27me3-npc_0.571

Matches to Query: 4_h_k27me3-npc_0.570

Matches to Query: 5_e_k27me3-npc_0.565

Matches to Query: 6_e_k27me3-npc_0.560

Matches to Query: 7_e_k27me3-h1_0.556

Summary

Alignment

Summary

Alignment

Matches to Query: 8_e_k27me3-h1_0.553

Matches to Query: 9_e_k27me3-h1_0.549

Matches to Query: 10_h_k27me3-h1_0.545

Matches to Query: 11_h_k27me3-h1_0.545

Matches to Query: 12_e_k27me3-npc_0.544

Matches to Query: 13_e_k27me3-h1_0.544

Matches to Query: 14_h_k27me3-npc_0.542

Matches to Query: 15_e_k27me3-npc_0.540

Matches to Query: 16_e_k27me3-npc_0.540

Matches to Query: 17_e_k27me3-h1_0.540

Matches to Query: 18_e_k27me3-h1_0.538

Matches to Query: 19_e_k27me3-npc_0.537

Summary

Alignment

Matches to Query: 20_e_k27me3-h1_0.526

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