Worm Phenotype (WP): early embryonic lethal

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Phenotype Ontology
Like Gene Ontology (GO), phenotypy 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. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
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)
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)
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 (YP)
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)
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)
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)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
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 (AP)
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 (EC)
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.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
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).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Root: WP Hierarchy (worm phenotype from Wormbase Release WS226)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
P-loop containing nucleoside triphosphate hydrolases	0	Direct
Histone-fold	0	Direct
Skp1 dimerisation domain-like	4.49e-16	Direct
ARM repeat	0.0000000000002001	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.000000000001172	Direct
GroEL-intermediate domain like	0.000000000178	Direct
GroEL equatorial domain-like	0.000000000178	Direct
GroEL apical domain-like	0.000000001646	Direct
Nucleic acid-binding proteins	0.00000001027	Direct
Zn-binding ribosomal proteins	0.00000003406	Direct
Class II aaRS and biotin synthetases	0.00000007861	Direct
Translation proteins SH3-like domain	0.0000008782	Direct
Tubulin C-terminal domain-like	0.000002303	Direct
S15/NS1 RNA-binding domain	0.000006177	Direct
TPR-like	0.000009708	Direct
Prefoldin	0.00001069	Direct
Activating enzymes of the ubiquitin-like proteins	0.00001069	Direct
"Winged helix" DNA-binding domain	0.00001135	Direct
Tubulin nucleotide-binding domain-like	0.0000165	Direct
Cyclin-like	0.00003604	Direct
Sm-like ribonucleoproteins	0.00004781	Direct
DNA ligase/mRNA capping enzyme, catalytic domain	0.00008111	Direct
ADC-like	0.00008111	Direct
Cdc48 domain 2-like	0.00008111	Direct
Class II aaRS ABD-related	0.0002566	Direct
CAD & PB1 domains	0.0003604	Direct
L30e-like	0.0005252	Direct
Translation proteins	0.0006765	Direct
Smc hinge domain	0.0009702	Direct
Translational machinery components	0.0009702	Direct
WD40 repeat-like	0.001904	Inherited
Calponin-homology domain, CH-domain	0.001954	Inherited
Nucleotidylyl transferase	0.004626	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.01322	Inherited
Invertebrate chitin-binding proteins	0.01814	Inherited
POZ domain	0.02975	Inherited
GTPase activation domain, GAP	0.03441	Inherited
UBC-like	0.1735	Inherited
BAR/IMD domain-like	0.2059	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.3002	Inherited

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Family

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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

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
P-loop containing nucleoside triphosphate hydrolases	0	Direct
Histone-fold	0	Direct
Skp1 dimerisation domain-like	3.517e-16	Direct
ARM repeat	0.0000000000001573	Direct
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.0000000000009235	Direct
GroEL equatorial domain-like	0.000000000141	Direct
GroEL-intermediate domain like	0.000000000141	Direct
GroEL apical domain-like	0.000000001308	Direct
Nucleic acid-binding proteins	0.000000008194	Direct
Zn-binding ribosomal proteins	0.00000002723	Direct
Class II aaRS and biotin synthetases	0.00000006296	Direct
Translation proteins SH3-like domain	0.0000007092	Direct
Tubulin C-terminal domain-like	0.000001866	Direct
S15/NS1 RNA-binding domain	0.000005021	Direct
TPR-like	0.000007897	Direct
Prefoldin	0.0000087	Direct
Activating enzymes of the ubiquitin-like proteins	0.0000087	Direct
"Winged helix" DNA-binding domain	0.00000924	Direct
Tubulin nucleotide-binding domain-like	0.00001344	Direct
Cyclin-like	0.00002943	Direct
Sm-like ribonucleoproteins	0.0000391	Direct
Cdc48 domain 2-like	0.00006638	Direct
DNA ligase/mRNA capping enzyme, catalytic domain	0.00006638	Direct
ADC-like	0.00006638	Direct
Class II aaRS ABD-related	0.0002111	Direct
CAD & PB1 domains	0.0002971	Direct
L30e-like	0.0004346	Direct
Translation proteins	0.0005611	Direct
Translational machinery components	0.0008075	Direct
Smc hinge domain	0.0008075	Direct
WD40 repeat-like	0.001596	Inherited
Calponin-homology domain, CH-domain	0.001638	Inherited
Nucleotidylyl transferase	0.003927	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.01142	Inherited
Invertebrate chitin-binding proteins	0.01576	Inherited
POZ domain	0.02611	Inherited
GTPase activation domain, GAP	0.03028	Inherited
UBC-like	0.1592	Inherited
BAR/IMD domain-like	0.1898	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.2811	Inherited

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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
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.000000000141	Direct
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical 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

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	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
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.000000000141	Direct

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Worm Phenotype (WP): early embryonic lethal

Superfamily

Family

Supra-domain (including individual superfamily)