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

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

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 Missing Motif crp Logo 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 Missing Motif nagC Logo 9 BP biofilm formation
BP peptidoglycan-based cell wall organization
BP peptidoglycan biosynthetic process
MF hydrolase activity, hydrolyzing O-glycosyl compounds
narP Missing Motif narP Logo 14 BP anaerobic respiration
MF molybdenum ion binding
BP cytochrome complex assembly
BP chemical homeostasis
BP cellular 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:0044248 1.341e-06 5.615e-07 4.559e-04 ~1% BP  cellular catabolic process deoC (25), fucP (51), fucA (52), uxaC (64), exuT (65), tdcA (71), rhaB (83), araB (144), fruB (147), fruB (148), ...42 more...
GO:0009056 8.869e-07 5.615e-07 4.559e-04 ~0% BP  catabolic process deoC (25), iraP (37), fucP (51), fucA (52), uxaC (64), exuT (65), tdcA (71), rhaB (83), araB (144), fruB (147), ...49 more...
GO:0008643 1.075e-04 1.011e-05 5.471e-03 ~4% BP  carbohydrate transport fucP (51), malK (138), malE (139), ulaA (174), xylF (179), idnD (197), yjjL (824)
GO:0051119 2.285e-04 2.302e-05 7.903e-03 ~5% MF  sugar transmembrane transporter activity fucP (51), glpT (99), malK (138), malE (139), xylF (179)
GO:0044275 2.652e-04 2.920e-05 7.903e-03 ~7% BP  cellular carbohydrate catabolic process fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), xylA (178), idnD (197), nanA (201), ...10 more...
GO:0015144 2.665e-04 2.920e-05 7.903e-03 ~3% MF  carbohydrate transmembrane transporter activity fucP (51), glpT (99), malK (138), malE (139), ulaA (174), xylF (179), ycaI (1391)
GO:0016861 3.954e-04 4.155e-05 9.640e-03 ~14% MF  intramolecular oxidoreductase activity, interconverting aldoses and ketoses fucP (51), uxaC (64), rhaB (83), srlA (111), araB (144), nagB (153), xylA (178), hisL (641), yihU (858), rpiB (897), ...3 more...
GO:0016860 4.737e-04 5.615e-05 1.103e-02 ~4% MF  intramolecular oxidoreductase activity fucP (51), uxaC (64), rhaB (83), srlA (111), araB (144), nagB (153), xylA (178), hisL (641), yihU (858), rpiB (897), ...4 more...
GO:0016052 5.421e-04 6.120e-05 1.103e-02 ~3% BP  carbohydrate catabolic process fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), ybjQ (158), xylA (178), idnD (197), ...14 more...
GO:0009057 5.850e-04 6.794e-05 1.103e-02 ~2% BP  macromolecule catabolic process iraP (37), fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), ybjQ (158), xylA (178), ...20 more...
GO:0016853 7.322e-04 9.208e-05 1.360e-02 ~1% MF  isomerase activity fucP (51), uxaC (64), yqcC (77), rhaB (83), srlA (111), araB (144), nagB (153), xylA (178), nanA (201), nanC (239), ...27 more...
GO:0044265 8.893e-04 1.185e-04 1.603e-02 ~6% BP  cellular macromolecule catabolic process fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), xylA (178), idnD (197), nanA (201), ...13 more...
GO:0019321 1.272e-03 1.926e-04 2.406e-02 ~16% BP  pentose metabolic process fucP (51), fucA (52), rhaB (83), araB (144), xylA (178), rbsD (364), aldA (1071), yiaK (1938)

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 1.011e-05 1.596e-02 ~0% BP  multi-organism process srlA (79), solA (181), yjbE (305), bhsA (376), ymgC (387), dcuB (442), yihR (478), hlyE (536), ttdA (588), zwf (720), ...3 more...
GO:0042710 4.020e-04 2.864e-05 2.262e-02 ~15% BP  biofilm formation srlA (79), solA (181), yjbE (305), bhsA (376), ymgC (387), dcuB (442), yihR (478), ttdA (588), ymgA (821), yjiP (889), ...1 more...
GO:0031504 8.308e-04 1.016e-04 2.293e-02 100% BP  peptidoglycan-based cell wall organization mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0009252 8.308e-04 1.016e-04 2.293e-02 ~89% BP  peptidoglycan biosynthetic process mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0009273 8.308e-04 1.016e-04 2.293e-02 ~29% BP  peptidoglycan-based cell wall biogenesis mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0007047 8.308e-04 1.016e-04 2.293e-02 ~37% BP  cellular cell wall organization mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0042546 8.308e-04 1.016e-04 2.293e-02 ~8% BP  cell wall biogenesis mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0016798 1.101e-03 1.482e-04 2.602e-02 ~1% MF  hydrolase activity, acting on glycosyl bonds chiA (11), uidA (95), mltA (98), essD (386)
GO:0004553 1.101e-03 1.482e-04 2.602e-02 ~2% MF  hydrolase activity, hydrolyzing O-glycosyl compounds chiA (11), uidA (95), mltA (98), essD (386)

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 5.109e-05 4.217e-02 ~54% BP  anaerobic respiration fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), lldP (715), narZ (798), zwf (2156), ...1 more...
GO:0045333 5.182e-04 7.805e-05 4.217e-02 15% BP  cellular respiration fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (672), lldP (715), narZ (798), cyoA (984), ...5 more...
GO:0030151 6.633e-04 9.770e-05 4.217e-02 100% MF  molybdenum ion binding fdnG (3), narG (21), dmsA (32), torC (228), narZ (798)
GO:0015980 9.717e-04 1.561e-04 4.217e-02 ~6% BP  energy derivation by oxidation of organic compounds fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (672), lldP (715), narZ (798), cyoA (984), ...6 more...
GO:0006091 9.717e-04 1.561e-04 4.217e-02 ~4% BP  generation of precursor metabolites and energy fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (672), lldP (715), narZ (798), cyoA (984), ...6 more...
GO:0017004 1.063e-03 1.825e-04 4.217e-02 ~46% BP  cytochrome complex assembly napF (1), fdnG (3), narG (21), cydA (609), sdhC (672)
GO:0043623 1.063e-03 1.825e-04 4.217e-02 ~9% BP  cellular protein complex assembly napF (1), fdnG (3), narG (21), cydA (609), sdhC (672)
GO:0042592 1.382e-03 2.431e-04 4.217e-02 ~1% BP  homeostatic process aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), gadA (255), adiA (370), nhaA (532), kefA (565), mscL (821), ...3 more...
GO:0048878 1.382e-03 2.431e-04 4.217e-02 ~2% BP  chemical homeostasis aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), gadA (255), adiA (370), nhaA (532), kefA (565), mscL (821), ...3 more...
GO:0019725 1.382e-03 2.431e-04 4.217e-02 ~4% BP  cellular homeostasis aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), gadA (255), adiA (370), nhaA (532), kefA (565), mscL (821), ...3 more...
GO:0009055 1.539e-03 2.835e-04 4.472e-02 ~13% MF  electron carrier activity fdnG (3), narG (21), frdA (25), dmsA (32), torC (228), cydA (609), sdhC (672), narZ (798), cyoA (984), ndh (1013), ...4 more...
GO:0065007 1.695e-03 3.178e-04 4.594e-02 ~0% BP  biological regulation napF (1), aqpZ (28), nhaB (30), adiC (60), gadB (80), acnA (106), lptA (147), mscS (155), sohA (224), alaS (236), ...36 more...
GO:0065008 1.839e-03 3.487e-04 4.653e-02 ~0% BP  regulation of biological quality aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), sohA (224), gadA (255), adiA (370), nhaA (532), kefA (565), ...5 more...
GO:0043169 2.049e-03 3.902e-04 4.835e-02 ~9% MF  cation binding fdnG (3), nirB (9), narG (21), dmsA (32), uxaC (172), torC (228), alaS (236), nagB (246), yfdR (378), fucA (510), ...16 more...

GOMo version:
4.11.3 (Release date: Tue Feb 14 14:24:20 2017 -0800)

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:


Seed: 3285257477

Significance Threshold: 0.05