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Worm Phenotype (WP): early embryonic lethal 
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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 ]
Family( show details)
Highlighted in gray are those with FDR_all>0.001
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| a tRNA synthase domain | 0 | DIRECT |
| Nucleosome core histones | 0 | DIRECT |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0 | DIRECT |
| Proteasome subunits | 0 | DIRECT |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0 | DIRECT |
| Anticodon-binding domain of Class II aaRS | 0 | DIRECT |
| Skp1 dimerisation domain-like | 0.000000000000002504 | DIRECT |
| Extended AAA-ATPase domain | 0.000000000005676 | DIRECT |
| Group II chaperonin (CCT, TRIC), apical domain | 0.0000000008215 | DIRECT |
| Armadillo repeat | 0.000000003986 | DIRECT |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.0000001079 | DIRECT |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.000001153 | DIRECT |
| Cyclin | 0.000001296 | DIRECT |
| BTB/POZ domain | 0.000004611 | DIRECT |
| Prefoldin | 0.000007228 | DIRECT |
| Tubulin, C-terminal domain | 0.000009387 | DIRECT |
| Ubiquitin activating enzymes (UBA) | 0.0000126 | DIRECT |
| Motor proteins | 0.00002334 | DIRECT |
| Tubulin, GTPase domain | 0.00005511 | DIRECT |
| Cdc48 domain 2-like | 0.0001358 | DIRECT |
| Cdc48 N-terminal domain-like | 0.0001358 | DIRECT |
| Pumilio repeat | 0.0001591 | DIRECT |
| G proteins | 0.0001661 | DIRECT |
| Translational machinery components | 0.0005072 | DIRECT |
| L30e/L7ae ribosomal proteins | 0.0005995 | DIRECT |
| Smc hinge domain | 0.0005995 | DIRECT |
| DEP domain | 0.0005995 | DIRECT |
| Sm motif of small nuclear ribonucleoproteins, SNRNP | 0.0009652 | DIRECT |
| Cold shock DNA-binding domain-like | 0.001083 | INHERITED FROM: pleiotropic defects severe early emb || other abnormality early emb |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.001121 | INHERITED FROM: pleiotropic defects severe early emb || other abnormality early emb |
| Actin/HSP70 | 0.00148 | INHERITED FROM: cleavage furrow defective early emb |
| WD40-repeat | 0.004242 | INHERITED FROM: cytoplasmic morphology defective early emb |
| Calponin-homology domain, CH-domain | 0.005464 | INHERITED FROM: cleavage furrow defective early emb || cleavage furrow initiation defective early emb |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.01498 | INHERITED FROM: pleiotropic defects severe early emb || other abnormality early emb |
| BCR-homology GTPase activation domain (BH-domain) | 0.06083 | INHERITED FROM: cleavage furrow defective early emb |
| PDZ domain | 0.09179 | INHERITED FROM: spindle defective early emb || mitotic spindle defective early emb |
| UBC-related | 0.2958 | INHERITED FROM: one cell arrest early emb |
| Protein serine/threonine phosphatase | 0.3053 | INHERITED FROM: meiosis defective early emb |
| Multidrug efflux transporter AcrB transmembrane domain | 0.3438 | INHERITED FROM: egg integrity defective early emb || embryo osmotic integrity defective early emb |
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| a tRNA synthase domain | 0 | Direct |
| Nucleosome core histones | 0 | Direct |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0 | Direct |
| Proteasome subunits | 0 | Direct |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0 | Direct |
| Anticodon-binding domain of Class II aaRS | 0 | Direct |
| Skp1 dimerisation domain-like | 0.000000000000002504 | Direct |
| Extended AAA-ATPase domain | 0.000000000005676 | Direct |
| Group II chaperonin (CCT, TRIC), apical domain | 0.0000000008215 | Direct |
| Armadillo repeat | 0.000000003986 | Direct |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.0000001079 | Direct |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.000001153 | Direct |
| Cyclin | 0.000001296 | Direct |
| BTB/POZ domain | 0.000004611 | Direct |
| Prefoldin | 0.000007228 | Direct |
| Tubulin, C-terminal domain | 0.000009387 | Direct |
| Ubiquitin activating enzymes (UBA) | 0.0000126 | Direct |
| Motor proteins | 0.00002334 | Direct |
| Tubulin, GTPase domain | 0.00005511 | Direct |
| Cdc48 domain 2-like | 0.0001358 | Direct |
| Cdc48 N-terminal domain-like | 0.0001358 | Direct |
| Pumilio repeat | 0.0001591 | Direct |
| G proteins | 0.0001661 | Direct |
| Translational machinery components | 0.0005072 | Direct |
| L30e/L7ae ribosomal proteins | 0.0005995 | Direct |
| Smc hinge domain | 0.0005995 | Direct |
| DEP domain | 0.0005995 | Direct |
| Sm motif of small nuclear ribonucleoproteins, SNRNP | 0.0009652 | Direct |
| Cold shock DNA-binding domain-like | 0.001083 | Inherited |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.001121 | Inherited |
| Actin/HSP70 | 0.00148 | Inherited |
| WD40-repeat | 0.004242 | Inherited |
| Calponin-homology domain, CH-domain | 0.005464 | Inherited |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.01498 | Inherited |
| BCR-homology GTPase activation domain (BH-domain) | 0.06083 | Inherited |
| PDZ domain | 0.09179 | Inherited |
| UBC-related | 0.2958 | Inherited |
| Protein serine/threonine phosphatase | 0.3053 | Inherited |
| Multidrug efflux transporter AcrB transmembrane domain | 0.3438 | Inherited |
LINKTO: Domain2BO Download and Domain2BO Algorithm
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Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
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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) |
56091,50249
56091 - DNA ligase/mRNA capping enzyme, catalytic domain
50249 - Nucleic acid-binding proteins | 0 | DIRECT |
54585,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
50692,54585
50692 - ADC-like
54585 - Cdc48 domain 2-like | 0 | DIRECT |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 0.000000000000001055 | DIRECT |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.000000000141 | DIRECT |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.000000000141 | DIRECT |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.000003679 | DIRECT |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.00001344 | DIRECT |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.00001344 | DIRECT |
55681,52954
55681 - Class II aaRS and biotin synthetases
52954 - Class II aaRS ABD-related | 0.00006638 | DIRECT |
48452,48452
48452 - TPR-like
48452 - TPR-like | 0.0002968 | DIRECT |
52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.08228 | INHERITED FROM: meiotic spindle defective early emb |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
56091,50249
56091 - DNA ligase/mRNA capping enzyme, catalytic domain
50249 - Nucleic acid-binding proteins | 0 | Direct |
54585,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
50692,54585
50692 - ADC-like
54585 - Cdc48 domain 2-like | 0 | Direct |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 0.000000000000001055 | Direct |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.000000000141 | Direct |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.000000000141 | Direct |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.000003679 | Direct |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.00001344 | Direct |
52490,55307
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like | 0.00001344 | Direct |
55681,52954
55681 - Class II aaRS and biotin synthetases
52954 - Class II aaRS ABD-related | 0.00006638 | Direct |
48452,48452
48452 - TPR-like
48452 - TPR-like | 0.0002968 | Direct |
52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.08228 | 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
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
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Plot tree as:
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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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> BO Hierarchy > early embryonic lethal
