Tomtom outputs a tab-separated values (TSV) file ('tomtom.tsv') that contains one line for each motif
found to be significantly enriched.
The lines are grouped by query motif and sorted in order of decreasing statistical significance.
The first line contains the (tab-separated) names of the fields.
Your command line is given at the end of the file in a comment line starting with the character '#'.
The names and meanings of each of the fields are described in the table below.
| field | name | contents |
| 1 | Query_ID |
The name of the query motif, which is unique in the motif database file.
|
| 2 | Target_ID |
The name of the target motif, which is unique in the motif database file.
|
| 3 | Optimal_offset |
The offset of the query motif relative to the target motif in the optimal alignment.
A positive value indicates the query is shifted right.
|
| 4 | p-value |
The probability that a random motif of the same width as the target would have an
optimal alignment with a match score as good or better than the target's.
Tomtom estimates the p-value using a null model consisting of sampling
motif columns from all the columns in the set of target motifs.
|
| 5 | E-value |
The expected number of false positives in the matches up to this point.
Tomtom estimates the E-value by multiplying the p-value by
the total number of target motifs in all the target databases.
|
| 6 | q-value |
The minimum False Discovery Rate (FDR) required to consider this match significant.
Tomtom estimates q-values from all the match p-values
using the method proposed by Benjamini & Hochberg (Journal of the Royal Statistical Society B, 57:289-300, 1995).
See also Storey JD, Tibshirani R. Statistical significance for
genome-wide studies, Proc. Natl. Acad. Sci. USA (2003) 100:9440–9445.
|
| 7 | Overlap |
The number of motif columns that overlap in the optimal alignment.
|
| 8 | Query_consensus | A consensus sequence
computed from the letter frequencies in the query motif
(as described below). |
| 9 | Target_consensus | A consensus sequence
computed from the letter frequencies in the target motif
(as described below). |
| 10 | Orientation |
The orientation of the target motif that gave the optimal alignment.
A value of '+' means that the target motif is as it appears in the database. A value of '-' means that the reverse complement of the target motif is shown.
|
The name of a file of motifs ("motif database file") that contains the query motif(s). Tomtom removes the '.meme' file name extension, if present.
The name of the query motif, which is unique in the motif database file.
An alternate name for the query motif, which may be provided in the motif database file.
A link to more information about the query motif.
A consensus sequence is constructed from each column in a
motif's frequency matrix using the "50% rule"
as follows:
- The letter frequencies in the column are sorted in decreasing order.
- Letters with frequency less 50% of the maximum are discarded.
- The letter used in this position in the consensus sequence is determined
by the first rule below that applies:
- If there is only one letter left, or if the remaining letters exactly match
an ambiguous symbol in the alphabet, the letter or ambiguous symbol,
respectively, is used.
- Otherwise, if the remaining set contains at least 50% of the core
symbols in the alphabet, the alphabet's wildcard
(e.g., "N" for DNA or RNA, and "X" for protein) is used.
- Otherwise, the letter with the maximum frequency is used.
The motif preview. On supporting browsers this will display as a motif
logo, otherwise the consensus sequence will be displayed.
The number motifs in the target database with a significant match to the query motif.
Links to the (up to) twenty target motifs with the most significant matches to the query motif.
The name of a file of motifs ("motif database file") that contains target motifs. Tomtom removes the '.meme' file name extension, if present.
The number of motifs read from the motif database minus the number that
had to be discarded due to conflicting IDs.
The number of motifs in this database that have a significant match to at least one of the query motifs.
The summary gives information about the target motif. Mouse over each
row to show further help buttons for each specific title.
The ID of the target motif with the optional alternate ID shown in parentheses.
The name of a file of motifs ("motif database file") that contains the matched motif. Tomtom removes the '.meme' file name extension, if present.
The probability that a random motif of the same width as the target would have an
optimal alignment with a match score as good or better than the target's.
Tomtom estimates the p-value using a null model consisting of sampling
motif columns from all the columns in the set of target motifs.
The expected number of false positives in the matches up to this point.
Tomtom estimates the E-value by multiplying the p-value by
the total number of target motifs in all the target databases.
The number of motif columns that overlap in the optimal alignment.
The offset of the query motif relative to the target motif in the optimal alignment.
A positive value indicates the query is shifted right.
The orientation of the target motif that gave the optimal alignment.
A value of 'Normal' means that the target motif is as it appears in the database. A value of 'Reverse Complement' means that the reverse complement of the target motif is shown.
The image shows the optimal alignment of the two motifs. The sequence logo
of the target motif is shown aligned above the logo for the query motif.
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.
Two image formats, png and eps, are available. 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.
Toggle error bars indicating the confidence of a motif based on the
number of sites used in its creation.
Toggle adding pseudocounts for Small Sample
Correction.
Toggle a full reverse complement of the alignment.
Specify the width of the generated logo.
Specify the height of the generated logo.
The name of the alphabet symbol.
The frequency of the alphabet symbol as defined by the background model.
Tomtom
Motif Comparison Tool
For further information on how to interpret these results please access
http://meme-suite.org/doc/tomtom-output-format.html.
To get a copy of the MEME software please access
http://meme-suite.org.
If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble,
"Quantifying similarity between motifs",
Genome Biology, 8(2):R24, 2007.
[full text]
| Database |
ID |
Alt. ID |
Preview |
Matches |
List |
| kernel-212.sel.ppm |
0000_35094_13.6106_4.8192_015_025 |
|
|
5 |
|
| kernel-212.sel.ppm |
0001_26338_13.3128_11.3889_008_026 |
|
|
68 |
MA0080.5 (SPI1), MA0765.2 (ETV5), MA0645.1 (ETV6), MA0750.2 (ZBTB7A), MA0081.2 (SPIB), MA0687.1 (SPIC), MA0080.3 (Spi1), MA0062.2 (Gabpa), MA0598.3 (EHF), MA0473.1 (ELF1), MA0136.2 (ELF5), MA0641.1 (ELF4), MA0640.2 (ELF3), MA0076.2 (ELK4), MA0473.3 (ELF1), MA0062.3 (GABPA), MA0062.1 (GABPA), MA0763.1 (ETV3), MA0473.2 (ELF1), MA1483.1 (ELF2), MA0014.1 (Pax5), MA0068.1 (Pax4), MA0615.1 (Gmeb1), MA0761.2 (ETV1), MA0759.1 (ELK3), MA0508.1 (PRDM1), MA0019.1 (Ddit3::Cebpa), MA0598.2 (EHF), MA0080.4 (SPI1), MA0760.1 (ERF), MA0028.2 (ELK1), MA0156.2 (FEV), MA0765.1 (ETV5), MA0673.1 (NKX2-8), MA0761.1 (ETV1), MA0764.1 (ETV4), MA0080.2 (SPI1), MA0098.3 (ETS1), MA0474.2 (ERG), MA0122.1 (Nkx3-2), MA1523.1 (MSANTD3), MA0114.4 (HNF4A), MA0484.2 (HNF4G), MA0640.1 (ELF3), MA0003.2 (TFAP2A), MA0050.2 (IRF1), MA0080.1 (SPI1), MA0475.2 (FLI1), MA0475.1 (FLI1), MA0114.2 (HNF4A), MA1652.1 (ZKSCAN5), MA1560.1 (SOHLH2), MA0098.2 (Ets1), MA0830.2 (TCF4), MA0028.1 (ELK1), MA0140.1 (Tal1::Gata1), MA0131.1 (HINFP), MA0484.1 (HNF4G), MA1631.1 (ASCL1(var.2)), MA0112.2 (ESR1), MA0508.2 (PRDM1), MA0506.1 (NRF1), MA0140.2 (GATA1::TAL1), MA0076.1 (ELK4), MA0693.2 (VDR), MA0527.1 (ZBTB33), MA0474.1 (Erg), MA1106.1 (HIF1A) |
| kernel-212.sel.ppm |
0002_24288_11.0128_10.8176_002_028 |
|
|
67 |
MA0527.1 (ZBTB33), MA0749.1 (ZBED1), MA1137.1 (FOSL1::JUNB), MA1622.1 (Smad2::Smad3), MA0037.2 (GATA3), MA0099.3 (FOS::JUN), MA0491.2 (JUND), MA1141.1 (FOS::JUND), MA1634.1 (BATF), MA1132.1 (JUN::JUNB), MA1135.1 (FOSB::JUNB), MA0490.2 (JUNB), MA0477.2 (FOSL1), MA1144.1 (FOSL2::JUND), MA1128.1 (FOSL1::JUN), MA0462.2 (BATF::JUN), MA0482.1 (Gata4), MA1138.1 (FOSL2::JUNB), MA1134.1 (FOS::JUNB), MA1142.1 (FOSL1::JUND), MA0037.3 (GATA3), MA1130.1 (FOSL2::JUN), MA0491.1 (JUND), MA0835.2 (BATF3), MA1633.1 (BACH1), MA0841.1 (NFE2), MA0766.1 (GATA5), MA0496.3 (MAFK), MA0462.1 (BATF::JUN), MA0655.1 (JDP2), MA0140.2 (GATA1::TAL1), MA1101.1 (BACH2), MA0140.1 (Tal1::Gata1), MA0476.1 (FOS), MA0099.2 (FOS::JUN), MA0489.1 (JUN(var.2)), MA0036.3 (GATA2), MA0035.3 (Gata1), MA0591.1 (Bach1::Mafk), MA0150.2 (Nfe2l2), MA0035.2 (Gata1), MA0478.1 (FOSL2), MA0490.1 (JUNB), MA0477.1 (FOSL1), MA1104.1 (GATA6), MA0828.1 (SREBF2(var.2)), MA0496.2 (MAFK), MA1521.1 (MAFA), MA0663.1 (MLX), MA1520.1 (MAF), MA0829.1 (Srebf1(var.2)), MA0099.1 (JUN::FOS), MA0495.2 (MAFF), MA0482.2 (GATA4), MA0089.2 (NFE2L1), MA0035.4 (GATA1), MA0865.1 (E2F8), MA0758.1 (E2F7), MA0659.1 (MAFG), MA0766.2 (GATA5), MA1104.2 (GATA6), MA1101.2 (BACH2), MA0150.1 (NFE2L2), MA0632.1 (Tcfl5), MA0036.2 (GATA2), MA0501.1 (MAF::NFE2), MA0024.1 (E2F1) |
| kernel-212.sel.ppm |
0003_3510_10.2872_5.3863_012_027 |
|
|
19 |
MA0527.1 (ZBTB33), MA0749.1 (ZBED1), MA0620.3 (MITF), MA0632.1 (Tcfl5), MA0828.1 (SREBF2(var.2)), MA0864.2 (E2F2), MA0663.1 (MLX), MA0620.2 (MITF), MA0829.1 (Srebf1(var.2)), MA0470.2 (E2F4), MA0526.2 (USF2), MA0829.2 (SREBF1(var.2)), MA0470.1 (E2F4), MA1122.1 (TFDP1), MA0603.1 (Arntl), MA0520.1 (Stat6), MA0664.1 (MLXIPL), MA1579.1 (ZBTB26), MA0620.1 (Mitf) |
| Database |
Used |
Matched |
| motifDB.txt |
1011 |
149 |
Alphabet
Source: the query file
| Name | Bg. | | | | Bg. | Name |
|---|
| Adenine | 0.25 | A | ~ | T | 0.25 | Thymine |
| Cytosine | 0.25 | C | ~ | G | 0.25 | Guanine |
Other Settings
TOMTOM version
5.1.0 (Release date: Fri Oct 11 15:53:28 2019 -0700)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble,
"Quantifying similarity between motifs",
Genome Biology, 8(2):R24, 2007.
Command line
Result calculation took 10.563 seconds
|