Worm Phenotype (WP): programmed cell death variant

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).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
PX domain	0	Direct
RBP11-like subunits of RNA polymerase	0	Direct
DLC	0	Direct
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
VPS9 domain	0	Direct
Subdomain of clathrin and coatomer appendage domain	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Clathrin adaptor appendage domain	0	Direct
Skp1 dimerisation domain-like	0.00000000000007132	Direct
FYVE/PHD zinc finger	0.000000004054	Direct
Cullin homology domain	0.00000005514	Direct
GroEL apical domain-like	0.0000001616	Direct
beta and beta-prime subunits of DNA dependent RNA-polymerase	0.0000006966	Direct
PH domain-like	0.0000008618	Direct
GroEL-intermediate domain like	0.000001636	Direct
GroEL equatorial domain-like	0.000001636	Direct
Cullin repeat-like	0.000001636	Direct
ENTH/VHS domain	0.000007572	Direct
Histone-fold	0.00002237	Direct
Sm-like ribonucleoproteins	0.00007829	Direct
Nucleic acid-binding proteins	0.0001026	Direct
SH3-domain	0.0001026	Direct
DNA repair protein MutS, domain III	0.000106	Direct
5' to 3' exonuclease, C-terminal subdomain	0.000106	Direct
Integrin domains	0.000106	Direct
BAR/IMD domain-like	0.0003403	Direct
Activating enzymes of the ubiquitin-like proteins	0.0003537	Direct
WD40 repeat-like	0.0004628	Direct
F1F0 ATP synthase subunit C	0.0004671	Direct
Tubby C-terminal domain-like	0.0004671	Direct
Cupredoxins	0.0004671	Direct
Caspase-like	0.0004671	Direct
DEATH domain	0.0007194	Direct
SNARE-like	0.0009757	Direct
Sec1/munc18-like (SM) proteins	0.001254	Inherited
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0.001254	Inherited
Lamin A/C globular tail domain	0.002171	Inherited
SET domain	0.002621	Inherited
PIN domain-like	0.00472	Inherited
Hect, E3 ligase catalytic domain	0.007687	Inherited
Intermediate filament protein, coiled coil region	0.01654	Inherited
Chromo domain-like	0.1134	Inherited
Protein kinase-like (PK-like)	0.1207	Inherited
POZ domain	0.1529	Inherited
Saposin	0.2016	Inherited
ARM repeat	0.2262	Inherited
RNA-binding domain, RBD	0.3994	Inherited
PLP-dependent transferases	0.5468	Inherited
"Winged helix" DNA-binding domain	0.5519	Inherited
Metallo-dependent phosphatases	0.5662	Inherited
S-adenosyl-L-methionine-dependent methyltransferases	0.6336	Inherited
HLH, helix-loop-helix DNA-binding domain	0.8108	Inherited
Calcium ATPase, transmembrane domain M	0.8682	Inherited
Metal cation-transporting ATPase, ATP-binding domain N	0.8682	Inherited
Calcium ATPase, transduction domain A	0.8969	Inherited
Cysteine proteinases	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
PX domain	0	Direct
Cullin repeat	0	Direct
DLC	0	Direct
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Myotubularin-like phosphatases	0	Direct
SCF ubiquitin ligase complex WHB domain	0	Direct
Group II chaperonin (CCT, TRIC), intermediate domain	0	Direct
RNA-polymerase beta	0	Direct
Phoshoinositide 3-kinase (PI3K) helical domain	0	Direct
Integrin domains	0	Direct
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Arginine methyltransferase	0	Direct
FYVE, a phosphatidylinositol-3-phosphate binding domain	6.263e-16	Direct
Skp1 dimerisation domain-like	0.000000000000259	Direct
Group II chaperonin (CCT, TRIC), apical domain	0.0000001145	Direct
Cullin homology domain	0.0000001499	Direct
Group II chaperonin (CCT, TRIC), ATPase domain	0.000001076	Direct
RecA protein-like (ATPase-domain)	0.000001576	Direct
Nucleosome core histones	0.0000731	Direct
BTB/POZ domain	0.000143	Direct
Ephrin ectodomain	0.0001668	Direct
DNA repair protein MutS, domain III	0.0001668	Direct
5' to 3' exonuclease catalytic domain	0.0001668	Direct
Caspase catalytic domain	0.0001668	Direct
5' to 3' exonuclease, C-terminal subdomain	0.0001668	Direct
Cold shock DNA-binding domain-like	0.0002681	Direct
Clathrin adaptor core protein	0.0002708	Direct
SH3-domain	0.0006187	Direct
BAR domain	0.0007322	Direct
Ubiquitin activating enzymes (UBA)	0.0007322	Direct
F1F0 ATP synthase subunit C	0.0007322	Direct
Histone lysine methyltransferases	0.001031	Inherited
Phosphotyrosine-binding domain (PTB)	0.001271	Inherited
Sm motif of small nuclear ribonucleoproteins, SNRNP	0.001271	Inherited
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0.001952	Inherited
Sec1/munc18-like (SM) proteins	0.001952	Inherited
Armadillo repeat	0.006003	Inherited
Translational machinery components	0.007299	Inherited
Hect, E3 ligase catalytic domain	0.01186	Inherited
Proteasome subunits	0.01245	Inherited
Protein kinases, catalytic subunit	0.01397	Inherited
Intermediate filament protein, coiled coil region	0.0255	Inherited
Canonical RBD	0.4968	Inherited
ABC transporter ATPase domain-like	0.5595	Inherited
G proteins	0.7598	Inherited
HLH, helix-loop-helix DNA-binding domain	0.7898	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.8492	Inherited
Calcium ATPase, transduction domain A	0.8785	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Clathrin adaptor appendage domain	0	Direct
PX domain	0	Direct
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
Subdomain of clathrin and coatomer appendage domain	0	Direct
VPS9 domain	0	Direct
DLC	0	Direct
RBP11-like subunits of RNA polymerase	0	Direct
Skp1 dimerisation domain-like	0.000000000000056	Direct
FYVE/PHD zinc finger	0.000000003228	Direct
Cullin homology domain	0.00000004413	Direct
GroEL apical domain-like	0.0000001297	Direct
beta and beta-prime subunits of DNA dependent RNA-polymerase	0.0000005621	Direct
PH domain-like	0.000000696	Direct
Cullin repeat-like	0.000001324	Direct
GroEL equatorial domain-like	0.000001324	Direct
GroEL-intermediate domain like	0.000001324	Direct
ENTH/VHS domain	0.000006158	Direct
Histone-fold	0.00001823	Direct
Sm-like ribonucleoproteins	0.00006407	Direct
SH3-domain	0.00008405	Direct
Nucleic acid-binding proteins	0.00008405	Direct
Integrin domains	0.00008687	Direct
DNA repair protein MutS, domain III	0.00008687	Direct
5' to 3' exonuclease, C-terminal subdomain	0.00008687	Direct
BAR/IMD domain-like	0.0002805	Direct
Activating enzymes of the ubiquitin-like proteins	0.0002915	Direct
WD40 repeat-like	0.0003826	Direct
Tubby C-terminal domain-like	0.0003863	Direct
Caspase-like	0.0003863	Direct
Cupredoxins	0.0003863	Direct
F1F0 ATP synthase subunit C	0.0003863	Direct
DEATH domain	0.0005972	Direct
SNARE-like	0.000812	Direct
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0.001046	Inherited
Sec1/munc18-like (SM) proteins	0.001046	Inherited
Lamin A/C globular tail domain	0.001824	Inherited
SET domain	0.002208	Inherited
PIN domain-like	0.004007	Inherited
Hect, E3 ligase catalytic domain	0.00657	Inherited
Intermediate filament protein, coiled coil region	0.01436	Inherited
Chromo domain-like	0.1027	Inherited
Protein kinase-like (PK-like)	0.1096	Inherited
POZ domain	0.1395	Inherited
Saposin	0.1857	Inherited
ARM repeat	0.2093	Inherited
RNA-binding domain, RBD	0.3789	Inherited
PLP-dependent transferases	0.5249	Inherited
"Winged helix" DNA-binding domain	0.5301	Inherited
Metallo-dependent phosphatases	0.5443	Inherited
S-adenosyl-L-methionine-dependent methyltransferases	0.6117	Inherited
HLH, helix-loop-helix DNA-binding domain	0.7927	Inherited
Calcium ATPase, transmembrane domain M	0.8519	Inherited
Metal cation-transporting ATPase, ATP-binding domain N	0.8519	Inherited
Calcium ATPase, transduction domain A	0.8817	Inherited
Cysteine proteinases	1	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	Direct
74788,75632 74788 - Cullin repeat-like 75632 - Cullin homology domain	0	Direct
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	Direct
49562,48371 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat	0	Direct
49348,55711 49348 - Clathrin adaptor appendage domain 55711 - Subdomain of clathrin and coatomer appendage domain	0	Direct
54695,81382 54695 - POZ domain 81382 - Skp1 dimerisation domain-like	0.0000000000001503	Direct
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.000001324	Direct
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.000001324	Direct
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00008687	Direct
81333,81333 81333 - F1F0 ATP synthase subunit C 81333 - F1F0 ATP synthase subunit C	0.00008687	Direct
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.01063	Inherited
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.03474	Inherited
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0.8519	Inherited
48371,56112 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0.9433	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49562,48371,56112 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 48371 - ARM repeat 56112 - Protein kinase-like (PK-like)	0	Direct
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	Direct
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.000001324	Direct
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0.01436	Inherited
81660,56784,81665 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0.8519	Inherited