The name (or number) identifying the motif in the input files.

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The visual representation of the position weight matrix otherwise known as the motif logo.

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The number of term predictions.

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If specificity data is avaliable then this displays the top 5 specific predictions, otherwise it just displays the top 5 predictions.

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The Gene Ontology Consortium term for a specific role or locality. Used for annotating genes with their purposes.

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A score generated as the geometric mean of rank-sum test(s) for the particular Gene Ontology term. The two groups compared by the rank-sum test are scores of genes annotated with the GO term and scores of genes not annotated with the GO term.

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An empirically generated p-value. The null hypothesis is that by shuffling the labels on gene scores, any possible association between the set of genes that a GO term annotates is destroyed. A large number of scores are generated using the null hypothesis and the number of null hypotheis scores that are better than each of the real scores is summed and then divided by the total null hypothesis scores generated to calculate a p-value.

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An empirically generated q-value. The q-values are calculated from the p-values using the method proposed by Benjamini & Hochberg (1995).

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A measure of the relative position in the GO hierarchy showing how specific a term is. A value of 100% implies that the GO term is the most specific form whereas a value of 0% implies that the GO term is one of the three roots of the Gene Ontology with only terms below it. A tilda (~) infront of the percentage implies that the value shown has been rounded and is not exact.

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The Gene Ontology hierarchy and Gene Ontology name of the term. The hierarchy is specified by the abbreviations BP for biological process, CC for cellular component and MF for molecular function.

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Gene name and rank of (up to) top 10 genes annotated with the GO term for the primary species.

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# GOMo

## Gene Ontology for Motifs

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu.

If you use GOMo in your research, please cite the following paper:
Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26(7), 860-866, 2010. [full text]

Investigated Motifs | Program information

## Investigated Motifs

#### Overview

Motif | Logo | Predictions | Top 5 specific predictions
--- | --- | --- | ---
crp |  | 13 | BP carbohydrate transport MF sugar transmembrane transporter activity BP cellular carbohydrate catabolic process MF intramolecular oxidoreductase activity, interconverting aldoses and ketoses BP cellular macromolecule catabolic process
nagC |  | 9 | BP biofilm formation BP peptidoglycan biosynthetic process BP peptidoglycan-based cell wall organization MF hydrolase activity, hydrolyzing O-glycosyl compounds
narP |  | 13 | BP anaerobic respiration MF molybdenum ion binding BP cytochrome complex assembly BP cellular homeostasis BP chemical homeostasis

## Motif crp | Next Top

GO terms are shown in grey if a more specific GO term was also significantly associated with this motif. The most specific GO terms are shown in black.
BP stands for biological process, CC stands for cellular component and MF stands for molecular function.

GO term | score | p-value | q-value | Specificity | GO name | Gene ID / Rank (2518 genes in total)
--- | --- | --- | --- | --- | --- | ---
GO:0009056 | 8.869e-07 | 5.615e-07 | 4.550e-04 | ~0% | BP | catabolic process | deoC (24), iraP (31), fucA (51), fucP (52), exuT (64), uxaC (65), tdcA (71), rhaB (80), araB (143), fruB (147), ...49 more...
GO:0044248 | 1.341e-06 | 5.615e-07 | 4.550e-04 | ~1% | BP | cellular catabolic process | deoC (24), fucA (51), fucP (52), exuT (64), uxaC (65), tdcA (71), rhaB (80), araB (143), fruB (147), fruB (148), ...42 more...
GO:0008643 | 1.075e-04 | 8.422e-06 | 4.550e-03 | ~4% | BP | carbohydrate transport | fucP (52), malE (135), malK (136), ulaA (172), xylF (177), idnD (196), yjjL (840)
GO:0051119 | 2.285e-04 | 2.077e-05 | 7.583e-03 | ~5% | MF | sugar transmembrane transporter activity | fucP (52), glpT (99), malE (135), malK (136), xylF (177)
GO:0044275 | 2.652e-04 | 2.695e-05 | 7.583e-03 | ~7% | BP | cellular carbohydrate catabolic process | fucA (51), fucP (52), rhaB (80), araB (143), fruB (147), fruB (148), nagB (153), xylA (176), idnD (196), nanA (204), ...10 more...
GO:0015144 | 2.665e-04 | 2.807e-05 | 7.583e-03 | ~3% | MF | carbohydrate transmembrane transporter activity | fucP (52), glpT (99), malE (135), malK (136), ulaA (172), xylF (177), ycaI (1391)
GO:0016861 | 3.954e-04 | 4.604e-05 | 1.058e-02 | ~14% | MF | intramolecular oxidoreductase activity, interconverting aldoses and ketoses | fucP (52), uxaC (65), rhaB (80), srlA (111), araB (143), nagB (153), xylA (176), hisL (637), yihU (858), rpiB (895), ...3 more...
GO:0016860 | 4.737e-04 | 5.222e-05 | 1.058e-02 | ~4% | MF | intramolecular oxidoreductase activity | fucP (52), uxaC (65), rhaB (80), srlA (111), araB (143), nagB (153), xylA (176), hisL (637), yihU (858), rpiB (895), ...4 more...
GO:0016052 | 5.421e-04 | 6.176e-05 | 1.112e-02 | ~3% | BP | carbohydrate catabolic process | fucA (51), fucP (52), rhaB (80), araB (143), fruB (147), fruB (148), nagB (153), ybjQ (159), xylA (176), idnD (196), ...14 more...
GO:0009057 | 5.850e-04 | 6.962e-05 | 1.128e-02 | ~2% | BP | macromolecule catabolic process | iraP (31), fucA (51), fucP (52), rhaB (80), araB (143), fruB (147), fruB (148), nagB (153), ybjQ (159), xylA (176), ...20 more...
GO:0016853 | 7.322e-04 | 9.321e-05 | 1.373e-02 | ~1% | MF | isomerase activity | fucP (52), uxaC (65), yqcC (78), rhaB (80), srlA (111), araB (143), nagB (153), xylA (176), nanA (204), nanC (238), ...27 more...
GO:0044265 | 8.893e-04 | 1.157e-04 | 1.562e-02 | ~6% | BP | cellular macromolecule catabolic process | fucA (51), fucP (52), rhaB (80), araB (143), fruB (147), fruB (148), nagB (153), xylA (176), idnD (196), nanA (204), ...13 more...
GO:0019321 | 1.272e-03 | 1.752e-04 | 2.184e-02 | ~16% | BP | pentose metabolic process | fucA (51), fucP (52), rhaB (80), araB (143), xylA (176), rbsD (365), aldA (1059), yiaK (1950)

## Motif nagC | Previous Next Top

GO terms are shown in grey if a more specific GO term was also significantly associated with this motif. The most specific GO terms are shown in black.
BP stands for biological process, CC stands for cellular component and MF stands for molecular function.

GO term | score | p-value | q-value | Specificity | GO name | Gene ID / Rank (2518 genes in total)
--- | --- | --- | --- | --- | --- | ---
GO:0051704 | 1.801e-04 | 2.190e-05 | 2.269e-02 | ~0% | BP | multi-organism process | srlA (79), solA (182), yjbE (305), bhsA (374), ymgC (388), dcuB (442), yihR (478), hlyE (535), ttdA (589), zwf (720), ...3 more...
GO:0042710 | 4.020e-04 | 5.278e-05 | 2.269e-02 | ~15% | BP | biofilm formation | srlA (79), solA (182), yjbE (305), bhsA (374), ymgC (388), dcuB (442), yihR (478), ttdA (589), ymgA (822), yjiP (893), ...1 more...
GO:0007047 | 8.308e-04 | 1.089e-04 | 2.269e-02 | ~37% | BP | cellular cell wall organization | mltB (78), mltA (98), mipA (129), mraZ (166), zwf (720)
GO:0009252 | 8.308e-04 | 1.089e-04 | 2.269e-02 | ~89% | BP | peptidoglycan biosynthetic process | mltB (78), mltA (98), mipA (129), mraZ (166), zwf (720)
GO:0009273 | 8.308e-04 | 1.089e-04 | 2.269e-02 | ~29% | BP | peptidoglycan-based cell wall biogenesis | mltB (78), mltA (98), mipA (129), mraZ (166), zwf (720)
GO:0031504 | 8.308e-04 | 1.089e-04 | 2.269e-02 | 100% | BP | peptidoglycan-based cell wall organization | mltB (78), mltA (98), mipA (129), mraZ (166), zwf (720)
GO:0042546 | 8.308e-04 | 1.089e-04 | 2.269e-02 | ~8% | BP | cell wall biogenesis | mltB (78), mltA (98), mipA (129), mraZ (166), zwf (720)
GO:0004553 | 1.101e-03 | 1.617e-04 | 2.620e-02 | ~2% | MF | hydrolase activity, hydrolyzing O-glycosyl compounds | chiA (11), uidA (94), mltA (98), essD (384)
GO:0016798 | 1.101e-03 | 1.617e-04 | 2.620e-02 | ~1% | MF | hydrolase activity, acting on glycosyl bonds | chiA (11), uidA (94), mltA (98), essD (384)

## Motif narP | Previous Top

GO terms are shown in grey if a more specific GO term was also significantly associated with this motif. The most specific GO terms are shown in black.
BP stands for biological process, CC stands for cellular component and MF stands for molecular function.

GO term | score | p-value | q-value | Specificity | GO name | Gene ID / Rank (2518 genes in total)
--- | --- | --- | --- | --- | --- | ---
GO:0009061 | 3.737e-04 | 5.446e-05 | 4.021e-02 | ~54% | BP | anaerobic respiration | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), lldP (716), narZ (797), zwf (2161), ...1 more...
GO:0045333 | 5.182e-04 | 7.580e-05 | 4.021e-02 | 15% | BP | cellular respiration | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (674), lldP (716), narZ (797), cyoA (980), ...5 more...
GO:0030151 | 6.633e-04 | 9.938e-05 | 4.021e-02 | 100% | MF | molybdenum ion binding | fdnG (3), narG (21), dmsA (32), torC (228), narZ (797)
GO:0006091 | 9.717e-04 | 1.454e-04 | 4.021e-02 | ~4% | BP | generation of precursor metabolites and energy | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (674), lldP (716), narZ (797), cyoA (980), ...6 more...
GO:0015980 | 9.717e-04 | 1.454e-04 | 4.021e-02 | ~6% | BP | energy derivation by oxidation of organic compounds | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (674), lldP (716), narZ (797), cyoA (980), ...6 more...
GO:0017004 | 1.063e-03 | 1.623e-04 | 4.021e-02 | ~46% | BP | cytochrome complex assembly | napF (2), fdnG (3), narG (21), cydA (607), sdhC (674)
GO:0043623 | 1.063e-03 | 1.623e-04 | 4.021e-02 | ~9% | BP | cellular protein complex assembly | napF (2), fdnG (3), narG (21), cydA (607), sdhC (674)
GO:0019725 | 1.382e-03 | 2.442e-04 | 4.237e-02 | ~4% | BP | cellular homeostasis | aqpZ (27), nhaB (30), adiC (60), gadB (77), mscS (156), gadA (252), adiA (363), nhaA (533), kefA (566), mscL (823), ...3 more...
GO:0042592 | 1.382e-03 | 2.442e-04 | 4.237e-02 | ~1% | BP | homeostatic process | aqpZ (27), nhaB (30), adiC (60), gadB (77), mscS (156), gadA (252), adiA (363), nhaA (533), kefA (566), mscL (823), ...3 more...
GO:0048878 | 1.382e-03 | 2.442e-04 | 4.237e-02 | ~2% | BP | chemical homeostasis | aqpZ (27), nhaB (30), adiC (60), gadB (77), mscS (156), gadA (252), adiA (363), nhaA (533), kefA (566), mscL (823), ...3 more...
GO:0009055 | 1.539e-03 | 2.858e-04 | 4.507e-02 | ~13% | MF | electron carrier activity | fdnG (3), narG (21), frdA (25), dmsA (32), torC (228), cydA (607), sdhC (674), narZ (797), cyoA (980), ndh (1014), ...4 more...
GO:0065007 | 1.695e-03 | 3.273e-04 | 4.732e-02 | ~0% | BP | biological regulation | napF (2), aqpZ (27), nhaB (30), adiC (60), gadB (77), acnA (106), lptA (145), mscS (156), sohA (226), alaS (236), ...36 more...
GO:0065008 | 1.839e-03 | 3.734e-04 | 4.982e-02 | ~0% | BP | regulation of biological quality | aqpZ (27), nhaB (30), adiC (60), gadB (77), mscS (156), sohA (226), gadA (252), adiA (363), nhaA (533), kefA (566), ...5 more...

GOMo version:
4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000)
Reference:
Mikael Bodén and Timothy L. Bailey, "Associating transcription factor binding site motifs with target Go terms and target genes", Nucleic Acids Research, 36, 4108-4117, 2008. [full text]
Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26, 860-866, 2010. [full text]
Input Data:
go-term-sequence mapping: bacteria_escherichia_coli_k12_1000_199.na.csv
scored sequence file: ama.xml
Command line summary:
This information can also be useful in the event you wish to report a problem with the GOMo software.
Command:
gomo --oc gomo_example_output_files --dag go.dag --images . bacteria_escherichia_coli_k12_1000_199.na.csv ama.xml
Seed: 3993088087
Significance Threshold: 0.05