Worm Phenotype (WP): muscle cell morphology variant

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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).

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

Shortest distance to current term (+ for parents, - for children) WP term [WP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + 4: Variant [WBPhenotype:0000886] <2>

+ + + 3: morphology variant [WBPhenotype:0000520] <5> (443|528) (444|229|63)

+ + 2: cell morphology variant [WBPhenotype:0000533] <10> (104|103) (106|55|17)

+ 1: cell type morphology variant [WBPhenotype:0002108] <12> (77|76) (79|45|15)

0: muscle cell morphology variant [WBPhenotype:0000904] <4> (23|27) (23|16|6)

- 1: nonstriated muscle morphology variant [WBPhenotype:0000923] <3> (0|0) (0|0|0)

- 1: striated muscle morphology variant [WBPhenotype:0000924] <2> (20|23) (20|16|5)

- 1: muscle cell ultrastructure variant [WBPhenotype:0002131] (0|0) (0|0|0)

- 1: myopodia present [WBPhenotype:0001932] (2|4) (3|1|1)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Integrin domains	0	Direct
Calpain large subunit, middle domain (domain III)	0.000000494	Direct
Troponin coil-coiled subunits	0.000000494	Direct
Growth factor receptor domain	0.000002182	Direct
SH2 domain	0.00000663	Direct
PH domain-like	0.00001651	Direct
SH3-domain	0.00002444	Direct
Myosin rod fragments	0.0000448	Direct
Protein kinase-like (PK-like)	0.0003193	Direct
Immunoglobulin	0.0003202	Direct
EGF/Laminin	0.0004185	Direct
Spectrin repeat	0.0004331	Direct
Voltage-gated potassium channels	0.0009429	Direct
Second domain of FERM	0.001438	Inherited
Tropomyosin	0.004691	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.006187	Inherited
DBL homology domain (DH-domain)	0.00683	Inherited
Calponin-homology domain, CH-domain	0.009057	Inherited
Fibronectin type III	0.02427	Inherited
Glutathione synthetase ATP-binding domain-like	0.05124	Inherited
Cysteine-rich domain	0.1298	Inherited
L domain-like	0.3203	Inherited
Actin-like ATPase domain	0.3525	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Integrin domains	0	Direct
Laminin-type module	0.00000004272	Direct
Calpain large subunit, middle domain (domain III)	0.000001056	Direct
SH2 domain	0.000005267	Direct
Troponin I	0.00001554	Direct
SH3-domain	0.00001971	Direct
Calpain large subunit, catalytic domain (domain II)	0.00007966	Direct
Myosin rod fragments	0.00007972	Direct
Pleckstrin-homology domain (PH domain)	0.000133	Direct
Protein kinases, catalytic subunit	0.0001349	Direct
I set domains	0.0002868	Direct
Spectrin repeat	0.0003404	Direct
LIM domain	0.0003404	Direct
Second domain of FERM	0.001141	Inherited
Growth factor receptor domain	0.001331	Inherited
Third domain of FERM	0.003797	Inherited
Tropomyosin	0.003797	Inherited
DBL homology domain (DH-domain)	0.005598	Inherited
Calponin-homology domain, CH-domain	0.007586	Inherited
First domain of FERM	0.01246	Inherited
EF-hand modules in multidomain proteins	0.01246	Inherited
Synaptotagmin-like (S variant)	0.01598	Inherited
Fibronectin type III	0.02088	Inherited
PLC-like (P variant)	0.04019	Inherited
Laminin G-like module	0.04418	Inherited
Lamin A/C globular tail domain	0.04418	Inherited
Actin/HSP70	0.2649	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)
Integrin domains	0	Direct
Troponin coil-coiled subunits	0.000000398	Direct
Calpain large subunit, middle domain (domain III)	0.000000398	Direct
Growth factor receptor domain	0.000001769	Direct
SH2 domain	0.000005391	Direct
PH domain-like	0.00001345	Direct
SH3-domain	0.00001994	Direct
Myosin rod fragments	0.00003661	Direct
Protein kinase-like (PK-like)	0.0002631	Direct
Immunoglobulin	0.0002638	Direct
EGF/Laminin	0.0003456	Direct
Spectrin repeat	0.0003577	Direct
Voltage-gated potassium channels	0.0007845	Direct
Second domain of FERM	0.001201	Inherited
Tropomyosin	0.003982	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.005272	Inherited
DBL homology domain (DH-domain)	0.005827	Inherited
Calponin-homology domain, CH-domain	0.007774	Inherited
Fibronectin type III	0.02121	Inherited
Glutathione synthetase ATP-binding domain-like	0.04544	Inherited
Cysteine-rich domain	0.118	Inherited
L domain-like	0.3008	Inherited
Actin-like ATPase domain	0.3324	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
54001,49758 54001 - Cysteine proteinases 49758 - Calpain large subunit, middle domain (domain III)	0.0000001049	Direct
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.000008327	Direct
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0000223	Direct
90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments	0.0002387	Direct
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.0002979	Direct
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.0008605	Direct
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.001201	Inherited
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	0.001201	Inherited
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.003982	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.003982	Inherited
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.006319	Inherited
50044,50044 50044 - SH3-domain 50044 - SH3-domain	0.01299	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.01299	Inherited
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain	0.04544	Inherited
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.04544	Inherited
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.3324	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.0001059	Direct
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.001201	Inherited
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.001201	Inherited
54236,47031,50729 54236 - Ubiquitin-like 47031 - Second domain of FERM 50729 - PH domain-like	0.003982	Inherited
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.005552	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.005827	Inherited

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

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Worm Phenotype (WP): muscle cell morphology variant

Superfamily

Family

Supra-domain (including individual superfamily)