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Worm Phenotype (WP): locomotion variant  
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Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Biomedical ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
- Mouse Phenotype (MP) Ontology MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
- Worm Phenotype (WP) Ontology WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
- Yeast Phenotype (YP) Ontology Based on YP which is the major contributor to the ‘Ascomycete phenotype ontology’, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
- Fly Phenotype (FP) Ontology FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
- Fly Anatomy (FA) Ontology FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
- Zebrafish Anatomy (ZA) Ontology ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
- Arabidopsis Plant Ontology (AP) Ontology As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
- Enzyme Commission (EC) Ontology Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
- UniProtKB KeyWords (KW) Ontology Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
- CTD Diseases (CD) Ontology CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
- CTD Chemicals (CC) Ontology CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).
Jump to [ Top · Hierarchy · Annotations ]
Root: WP Hierarchy (worm phenotype from Wormbase Release WS226)
Jump to [ Top · Hierarchy ]
Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Duplex) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49493,49493 49493 - HSP40/DnaJ peptide-binding domain 49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
81383,50978 81383 - F-box domain 50978 - WD40 repeat-like | 0 | DIRECT |
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
49348,55711 49348 - Clathrin adaptor appendage domain 55711 - Subdomain of clathrin and coatomer appendage domain | 0 | DIRECT |
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region | 0 | DIRECT |
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
57938,49493 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like | 0 | DIRECT |
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | DIRECT |
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase | 0 | DIRECT |
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.0000000001393 | DIRECT |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.00000005998 | DIRECT |
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat | 0.000006556 | DIRECT |
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like | 0.00007622 | DIRECT |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.0005182 | DIRECT |
48371,48371 48371 - ARM repeat 48371 - ARM repeat | 0.0005593 | DIRECT |
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain | 0.003374 | INHERITED FROM: locomotion reduced || paralyzed |
47473,47473 47473 - EF-hand 47473 - EF-hand | 0.01199 | INHERITED FROM: sinusoidal movement variant || body bend variant |
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat | 0.01391 | INHERITED FROM: path curvature variant || sinusoidal movement variant || forward point velocity variant || frequency of body bend variant || backward locomotion variant || amplitude of sinusoidal movement variant || directionality variant || pausing variant || backing decreased || body bend variant || turning frequency variant || reversal variant || velocity of movement variant || turning variant || forward locomotion variant || backward point velocity variant |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.2505 | INHERITED FROM: paralyzed |
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.9153 | INHERITED FROM: forward point velocity variant || backward locomotion variant || amplitude of sinusoidal movement variant || locomotion reduced || locomotor coordination variant || turning frequency variant || reversal variant || forward locomotion decreased || turning variant || backward point velocity variant |
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin | 1 | INHERITED FROM: path curvature increased || forward point velocity variant || backward locomotion variant || amplitude of sinusoidal movement variant || locomotion reduced || body bend variant || locomotor coordination variant || turning frequency variant || reversal variant || turning variant || backward point velocity variant |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49493,49493 49493 - HSP40/DnaJ peptide-binding domain 49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
81383,50978 81383 - F-box domain 50978 - WD40 repeat-like | 0 | Direct |
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
49348,55711 49348 - Clathrin adaptor appendage domain 55711 - Subdomain of clathrin and coatomer appendage domain | 0 | Direct |
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region | 0 | Direct |
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
57938,49493 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like | 0 | Direct |
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | Direct |
55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase | 0 | Direct |
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like) | 0 | Direct |
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.0000000001393 | Direct |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.00000005998 | Direct |
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat | 0.000006556 | Direct |
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like | 0.00007622 | Direct |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.0005182 | Direct |
48371,48371 48371 - ARM repeat 48371 - ARM repeat | 0.0005593 | Direct |
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain | 0.003374 | Inherited |
47473,47473 47473 - EF-hand 47473 - EF-hand | 0.01199 | Inherited |
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat | 0.01391 | Inherited |
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.2505 | Inherited |
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.9153 | Inherited |
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin | 1 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Triple) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
55973,55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase | 0 | DIRECT |
57362,57362,57362 57362 - BPTI-like 57362 - BPTI-like 57362 - BPTI-like | 0 | DIRECT |
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
57938,49493,49493 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain 49493 - HSP40/DnaJ peptide-binding domain | 0 | DIRECT |
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | DIRECT |
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat | 0 | DIRECT |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.000002984 | DIRECT |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.000161 | DIRECT |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.1316 | INHERITED FROM: paralyzed |
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.9658 | INHERITED FROM: locomotion reduced |
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin | 1 | INHERITED FROM: forward point velocity variant || backward locomotion variant || amplitude of sinusoidal movement variant || locomotion reduced || body bend variant || turning frequency variant || reversal variant || turning variant || backward point velocity variant |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
55973,55973,55973 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase 55973 - S-adenosylmethionine synthetase | 0 | Direct |
57362,57362,57362 57362 - BPTI-like 57362 - BPTI-like 57362 - BPTI-like | 0 | Direct |
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
57938,49493,49493 57938 - DnaJ/Hsp40 cysteine-rich domain 49493 - HSP40/DnaJ peptide-binding domain 49493 - HSP40/DnaJ peptide-binding domain | 0 | Direct |
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | Direct |
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat | 0 | Direct |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.000002984 | Direct |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.000161 | Direct |
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module | 0.1316 | Inherited |
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III | 0.9658 | Inherited |
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin | 1 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Plot distribution on species Tree Of Life (sTOL) for Superfamily and/or Family domains annotated by this WP term
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Plot tree as:
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Download Newick format tree:
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( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Plot distribution on species Tree Of Life (sTOL) for single supra-domains annotated by this WP term
 |
Plot tree as:
| |
Download Newick format tree:
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Browsing in TREE OF LIFE:
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( show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
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