Worm Phenotype (WP): striated muscle morphology variant

(show info)

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)

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

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

+ + 2: organ system morphology variant [WBPhenotype:0000534] <9> (99|104) (101|47|17)

+ + 2: cell type morphology variant [WBPhenotype:0002108] <12> (77|76) (79|45|15)

+ 1: muscle system morphology variant [WBPhenotype:0000603] <2> (21|23) (21|16|5)

+ 1: muscle cell morphology variant [WBPhenotype:0000904] <4> (23|27) (23|16|6)

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

- 1: body wall muscle morphology variant [WBPhenotype:0000926] <3> (19|21) (19|15|4)

- 1: male longitudinal muscle morphology variant [WBPhenotype:0000927] (0|0) (0|0|0)

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

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Integrin domains	0	Direct
SH3-domain	0.00000000002704	Direct
Calponin-homology domain, CH-domain	0.00000001911	Direct
SH2 domain	0.00000006089	Direct
Spectrin repeat	0.0000001344	Direct
C2 domain (Calcium/lipid-binding domain, CaLB)	0.0000001418	Direct
Calpain large subunit, middle domain (domain III)	0.0000003132	Direct
Myosin rod fragments	0.00003096	Direct
Second domain of FERM	0.00008955	Direct
Tropomyosin	0.0001025	Direct
DBL homology domain (DH-domain)	0.000128	Direct
Voltage-gated potassium channels	0.0004781	Direct
Cysteine-rich domain	0.0006515	Direct
Actin-like ATPase domain	0.006835	Inherited
Glutathione synthetase ATP-binding domain-like	0.021	Inherited
Growth factor receptor domain	0.9703	Inherited
Immunoglobulin	1	Inherited
Troponin coil-coiled subunits	1	Inherited
Fibronectin type III	1	Inherited
EGF/Laminin	1	Inherited

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

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Integrin domains	0	Direct
SH3-domain	0.0000000003666	Direct
Pleckstrin-homology domain (PH domain)	0.0000000008115	Direct
Calponin-homology domain, CH-domain	0.00000008763	Direct
Spectrin repeat	0.0000001271	Direct
LIM domain	0.0000001271	Direct
SH2 domain	0.0000004553	Direct
Calpain large subunit, middle domain (domain III)	0.0000006569	Direct
Calpain large subunit, catalytic domain (domain II)	0.00005081	Direct
EF-hand modules in multidomain proteins	0.00005254	Direct
Myosin rod fragments	0.00005433	Direct
Third domain of FERM	0.0001028	Direct
Second domain of FERM	0.0001221	Direct
First domain of FERM	0.0001474	Direct
PLC-like (P variant)	0.0001779	Direct
Tropomyosin	0.0001779	Direct
DBL homology domain (DH-domain)	0.0002552	Direct
Lamin A/C globular tail domain	0.00103	Inherited
Synaptotagmin-like (S variant)	0.001284	Inherited
Actin/HSP70	0.001362	Inherited
Laminin-type module	1	Inherited
Fibronectin type III	1	Inherited
I set domains	1	Inherited

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

Plot tree as:

Download Newick format tree:

(show help)

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

Supra-domain (including individual superfamily)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Integrin domains	0	Direct
SH3-domain	0.00000000002136	Direct
Calponin-homology domain, CH-domain	0.00000001525	Direct
SH2 domain	0.00000004873	Direct
Spectrin repeat	0.0000001078	Direct
C2 domain (Calcium/lipid-binding domain, CaLB)	0.0000001137	Direct
Calpain large subunit, middle domain (domain III)	0.0000002519	Direct
Myosin rod fragments	0.00002528	Direct
Second domain of FERM	0.00007335	Direct
Tropomyosin	0.00008397	Direct
DBL homology domain (DH-domain)	0.000105	Direct
Voltage-gated potassium channels	0.0003955	Direct
Cysteine-rich domain	0.0005401	Direct
Actin-like ATPase domain	0.005831	Inherited
Glutathione synthetase ATP-binding domain-like	0.01829	Inherited
Growth factor receptor domain	0.9581	Inherited
Troponin coil-coiled subunits	1	Inherited
Immunoglobulin	1	Inherited
Fibronectin type III	1	Inherited
EGF/Laminin	1	Inherited

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.000000001484	Direct
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.00000006613	Direct
54001,49758 54001 - Cysteine proteinases 49758 - Calpain large subunit, middle domain (domain III)	0.00000006613	Direct
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.000006133	Direct
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	0.00001217	Direct
50044,50044 50044 - SH3-domain 50044 - SH3-domain	0.0001781	Direct
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain	0.0001781	Direct
90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments	0.0001781	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.0001781	Direct
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.0002121	Direct
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.0002121	Direct
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.0003369	Direct
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.002809	Inherited
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.9821	Inherited
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	1	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	1	Inherited

(show details)

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)	0.0000000001308	Direct
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.000000009911	Direct
54236,47031,50729 54236 - Ubiquitin-like 47031 - Second domain of FERM 50729 - PH domain-like	0.0001373	Direct
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.9332	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	1	Inherited

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

Plot tree as:

Download Newick format tree:

(show help)

SEARCH

BROWSE

TOOLS

ABOUT

HELP

Worm Phenotype (WP): striated muscle morphology variant

Superfamily

Family

Supra-domain (including individual superfamily)