TOMTOM

Name	Preview	Matches	List
1_h_k27me3_2_0.786	GCGCTACGCG	0
2_h_k4me3_9_0.748	CTTTCGCG	2	SWI4_MA0401.1_J, E2F_Q3_M00425_T
3_h_k4me3_4_0.709	CGGTAGTG	0
4_h_k4me3_10_0.699	CGTTTTCG	0
5_e_k4me3_31_0.697	ATGGCGGCG	1	ERF2_01_M01057_T
6_e_k4me3_73_0.687	CGTCATCGCG	1	CREB_Q3_M00801_T
7_h_k27me3_13_0.669	TTCGGAAA	2	BORG2_01_M01544_T, Cep3_GR09_U
8_e_k4me3_100_0.650	TCAGAGCGC	0
9_e_k36me3_192_0.646	ACGTAGCGA	0
10_e_k27ac_36_0.358	GCTGAGTCAG	11	MAF_Q6_01_M00983_T, NRF2_Q4_M00821_T, NFE2_01_M00037_T, NFE2L2_MA0150.1_J, VMAF_01_M00035_T, AP1_MA0099.2_J, AP1_Q6_M00174_T, TCF11MAFG_01_M00284_T, AP1_C_M00199_T, AP1_01_M00517_T
11_e_k36me3_89_0.361	ATCCCAGCA	0
12_e_k36me3_203_0.365	CAGGACCAG	0
13_e_k36me3_235_0.365	ATGCCACTGTT	0
14_e_k27me3_301_0.622	AATACGCGT	0
15_h_k9me3_27_0.384	CCCATGGG	1	GPAM_2_H
16_h_k4me3_21_0.605	TTTTTACCCG	0
17_h_k27ac_12_0.435	GGAATGTCACAA	0
18_h_k36me3_25_0.440	GCACCACATGCA	0
19_e_k9me3_180_0.450	GAAATCACCC	0
20_h_k9me3_13_0.523	GGTACCTCAG	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	18

Summary

Alignment

Name	SWI4_MA0401.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.88018e-06
E-value	0.020097
q-value	0.0235262
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	E2F_Q3_M00425_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.07272e-06
E-value	0.0265014
q-value	0.0235262
Overlap	7
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	ERF2_01_M01057_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.30211e-07
E-value	0.000964545
q-value	0.00192783
Overlap	7
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	CREB_Q3_M00801_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.53653e-06
E-value	0.0044882
q-value	0.00892577
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	BORG2_01_M01544_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.22908e-05
E-value	0.0359015
q-value	0.0325303
Overlap	8
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Cep3_GR09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.22908e-05
E-value	0.0359015
q-value	0.0325303
Overlap	8
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MAF_Q6_01_M00983_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.35461e-08
E-value	0.000214828
q-value	0.000313067
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	NRF2_Q4_M00821_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.07767e-07
E-value	0.000314789
q-value	0.000313067
Overlap	10
Offset	2
Orientation	Normal

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Summary

Alignment

Name	NFE2_01_M00037_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.71389e-07
E-value	0.000500627
q-value	0.000331926
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	NFE2L2_MA0150.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.3546e-07
E-value	0.00097988
q-value	0.00048726
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	VMAF_01_M00035_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.02121e-06
E-value	0.00590397
q-value	0.00234867
Overlap	10
Offset	4
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_MA0099.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.69593e-06
E-value	0.0078748
q-value	0.00238489
Overlap	7
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_M00174_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.15074e-06
E-value	0.0092033
q-value	0.00238489
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TCF11MAFG_01_M00284_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.28382e-06
E-value	0.00959203
q-value	0.00238489
Overlap	10
Offset	7
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_C_M00199_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.20381e-06
E-value	0.0268843
q-value	0.00594162
Overlap	9
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_01_M00517_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.14642e-05
E-value	0.0334871
q-value	0.00609219
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	FRA1_Q5_M01267_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.15342e-05
E-value	0.0336913
q-value	0.00609219
Overlap	8
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	GPAM_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.16269e-05
E-value	0.0339623
q-value	0.0679246
Overlap	5
Offset	0
Orientation	Reverse Complement

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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_2_0.786

Matches to Query: 2_h_k4me3_9_0.748

Summary

Alignment

Summary

Alignment

Matches to Query: 3_h_k4me3_4_0.709

Matches to Query: 4_h_k4me3_10_0.699

Matches to Query: 5_e_k4me3_31_0.697

Summary

Alignment

Matches to Query: 6_e_k4me3_73_0.687

Summary

Alignment

Matches to Query: 7_h_k27me3_13_0.669

Summary

Alignment

Summary

Alignment

Matches to Query: 8_e_k4me3_100_0.650

Matches to Query: 9_e_k36me3_192_0.646

Matches to Query: 10_e_k27ac_36_0.358

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 11_e_k36me3_89_0.361

Matches to Query: 12_e_k36me3_203_0.365

Matches to Query: 13_e_k36me3_235_0.365

Matches to Query: 14_e_k27me3_301_0.622

Matches to Query: 15_h_k9me3_27_0.384

Summary

Alignment

Matches to Query: 16_h_k4me3_21_0.605

Matches to Query: 17_h_k27ac_12_0.435

Matches to Query: 18_h_k36me3_25_0.440

Matches to Query: 19_e_k9me3_180_0.450

Matches to Query: 20_h_k9me3_13_0.523

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

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