Worm Phenotype (WP): metabolic pathway 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)
Heme-dependent catalase-like	0	Direct
Arginase/deacetylase	0.0000000001815	Direct
Lipovitellin-phosvitin complex, superhelical domain	0.0000004686	Direct
Lipovitellin-phosvitin complex; beta-sheet shell regions	0.0000004686	Direct
Protein kinase-like (PK-like)	0.00005289	Direct
ADC-like	0.00008175	Direct
Cdc48 domain 2-like	0.00008175	Direct
Integrin domains	0.00008175	Direct
Calpain large subunit, middle domain (domain III)	0.0001799	Direct
DHS-like NAD/FAD-binding domain	0.0001799	Direct
Translational machinery components	0.0008494	Direct
Zn-binding ribosomal proteins	0.0008494	Direct
L30e-like	0.0009659	Direct
SET domain	0.001428	Inherited
RNA-binding domain, RBD	0.00336	Inherited
PH domain-like	0.005975	Inherited
GroEL-intermediate domain like	0.007024	Inherited
GroEL equatorial domain-like	0.007024	Inherited
DNA/RNA polymerases	0.01047	Inherited
Spectrin repeat	0.01047	Inherited
GroEL apical domain-like	0.01377	Inherited
SH3-domain	0.01422	Inherited
F1F0 ATP synthase subunit C	0.01477	Inherited
Voltage-gated potassium channels	0.02294	Inherited
Translation proteins	0.03206	Inherited
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0.03448	Inherited
Quinoprotein alcohol dehydrogenase-like	0.03895	Inherited
Nucleic acid-binding proteins	0.1054	Inherited
Immunoglobulin	0.1266	Inherited
Clavaminate synthase-like	0.1717	Inherited
Cyclin-like	0.2547	Inherited
Sm-like ribonucleoproteins	0.3098	Inherited
Transducin (alpha subunit), insertion domain	0.3684	Inherited
Nucleotide cyclase	0.4172	Inherited
FYVE/PHD zinc finger	0.4305	Inherited
Periplasmic binding protein-like I	0.4749	Inherited
Cytochrome P450	0.6074	Inherited
Chromo domain-like	0.6827	Inherited
Homeodomain-like	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)
Sir2 family of transcriptional regulators	0	Direct
Heme-dependent catalases	0	Direct
Histone deacetylase, HDAC	0	Direct
Integrin domains	0	Direct
Lipovitellin-phosvitin complex, superhelical domain	0.000001116	Direct
Lipovitellin-phosvitin complex; beta-sheet shell regions	0.000001116	Direct
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.0000541	Direct
Cdc48 domain 2-like	0.000133	Direct
Cdc48 N-terminal domain-like	0.000133	Direct
Calpain large subunit, middle domain (domain III)	0.0001696	Direct
Proteasome subunits	0.0009902	Direct
Histone lysine methyltransferases	0.0009902	Direct
Calpain large subunit, catalytic domain (domain II)	0.001489	Inherited
Group II chaperonin (CCT, TRIC), intermediate domain	0.00358	Inherited
Spectrin repeat	0.003644	Inherited
Pleckstrin-homology domain (PH domain)	0.003697	Inherited
Protein kinases, catalytic subunit	0.004688	Inherited
Canonical RBD	0.005529	Inherited
I set domains	0.008424	Inherited
F1F0 ATP synthase subunit C	0.01384	Inherited
Group II chaperonin (CCT, TRIC), ATPase domain	0.02115	Inherited
Elongation factors	0.02382	Inherited
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0.0329	Inherited
G proteins	0.03688	Inherited
Group II chaperonin (CCT, TRIC), apical domain	0.03809	Inherited
LIM domain	0.06125	Inherited
Voltage-gated potassium channels	0.07839	Inherited
Cold shock DNA-binding domain-like	0.2575	Inherited
Transducin (alpha subunit), insertion domain	0.3708	Inherited
PHD domain	0.4094	Inherited
Adenylyl and guanylyl cyclase catalytic domain	0.5437	Inherited
Cytochrome P450	0.7798	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)
Heme-dependent catalase-like	0	Direct
Arginase/deacetylase	0.0000000001437	Direct
Lipovitellin-phosvitin complex, superhelical domain	0.0000003774	Direct
Lipovitellin-phosvitin complex; beta-sheet shell regions	0.0000003774	Direct
Protein kinase-like (PK-like)	0.00004328	Direct
ADC-like	0.00006692	Direct
Cdc48 domain 2-like	0.00006692	Direct
Integrin domains	0.00006692	Direct
DHS-like NAD/FAD-binding domain	0.0001477	Direct
Calpain large subunit, middle domain (domain III)	0.0001477	Direct
Translational machinery components	0.0007066	Direct
Zn-binding ribosomal proteins	0.0007066	Direct
L30e-like	0.0008038	Direct
SET domain	0.001193	Inherited
RNA-binding domain, RBD	0.00284	Inherited
PH domain-like	0.005087	Inherited
GroEL equatorial domain-like	0.005993	Inherited
GroEL-intermediate domain like	0.005993	Inherited
DNA/RNA polymerases	0.009014	Inherited
Spectrin repeat	0.009014	Inherited
GroEL apical domain-like	0.01192	Inherited
SH3-domain	0.0123	Inherited
F1F0 ATP synthase subunit C	0.01279	Inherited
Voltage-gated potassium channels	0.02002	Inherited
Translation proteins	0.02819	Inherited
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0.03034	Inherited
Quinoprotein alcohol dehydrogenase-like	0.03433	Inherited
Nucleic acid-binding proteins	0.09533	Inherited
Immunoglobulin	0.115	Inherited
Clavaminate synthase-like	0.1574	Inherited
Cyclin-like	0.2368	Inherited
Sm-like ribonucleoproteins	0.2905	Inherited
Transducin (alpha subunit), insertion domain	0.348	Inherited
Nucleotide cyclase	0.3965	Inherited
FYVE/PHD zinc finger	0.4097	Inherited
Periplasmic binding protein-like I	0.4536	Inherited
Cytochrome P450	0.5855	Inherited
Chromo domain-like	0.6614	Inherited
Homeodomain-like	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)
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	Direct
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain	0.0000003774	Direct
48431,56968 48431 - Lipovitellin-phosvitin complex, superhelical domain 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions	0.0000003774	Direct
54001,49758 54001 - Cysteine proteinases 49758 - Calpain large subunit, middle domain (domain III)	0.0001477	Direct
81333,81333 81333 - F1F0 ATP synthase subunit C 81333 - F1F0 ATP synthase subunit C	0.003327	Inherited
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.005993	Inherited
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.005993	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.009014	Inherited
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.01118	Inherited
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.01279	Inherited
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	0.02097	Inherited
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.08633	Inherited
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.1141	Inherited
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.348	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)
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat	0	Direct
56968,48431,56968 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions	0.0000003774	Direct
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.005993	Inherited
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.01279	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.01279	Inherited
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.05271	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)	0.09115	Inherited