Mammalian Phenotype (MP): abnormal muscle physiology

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)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
MIR domain	0.00004615	Direct
IP3 receptor type 1 binding core, domain 2	0.0000571	Direct
Voltage-gated potassium channels	0.001635	Inherited
Metal cation-transporting ATPase, ATP-binding domain N	0.001831	Inherited
SRF-like	0.002162	Inherited
WW domain	0.02013	Inherited
Transducin (alpha subunit), insertion domain	0.02375	Inherited
Inhibitor of apoptosis (IAP) repeat	0.0252	Inherited
Nucleotide cyclase	0.05966	Inherited
BPTI-like	0.07276	Inherited
Calcium ATPase, transduction domain A	0.0876	Inherited
Calcium ATPase, transmembrane domain M	0.0876	Inherited
E set domains	0.09482	Inherited
POZ domain	0.1378	Inherited
Lipocalins	0.206	Inherited
Flavoproteins	0.3853	Inherited
Myosin rod fragments	0.3912	Inherited
Riboflavin synthase domain-like	0.4686	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.4686	Inherited
Nuclear receptor ligand-binding domain	0.5254	Inherited
alpha-catenin/vinculin-like	0.6518	Inherited
L domain-like	0.8595	Inherited
HLH, helix-loop-helix DNA-binding domain	0.9647	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)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.00001954	Direct
Calcium ATPase, transmembrane domain M	0.00002706	Direct
MIR domain	0.00003183	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.00006104	Direct
Metal cation-transporting ATPase, ATP-binding domain N	0.0003939	Direct
SRF-like	0.001534	Inherited
Voltage-gated potassium channels	0.00315	Inherited
Tetramerization domain of potassium channels	0.003245	Inherited
alpha-catenin/vinculin	0.005193	Inherited
LIM domain	0.007646	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.01029	Inherited
Inhibitor of apoptosis (IAP) repeat	0.01139	Inherited
WW domain	0.01786	Inherited
Transducin (alpha subunit), insertion domain	0.01996	Inherited
Adenylyl and guanylyl cyclase catalytic domain	0.05234	Inherited
Small Kunitz-type inhibitors & BPTI-like toxins	0.06232	Inherited
Meta-cation ATPase, catalytic domain P	0.06663	Inherited
Calcium ATPase, transduction domain A	0.06663	Inherited
Fatty acid binding protein-like	0.1723	Inherited
Phosphotyrosine-binding domain (PTB)	0.2431	Inherited
NADPH-cytochrome p450 reductase-like	0.3442	Inherited
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.3442	Inherited
Cytochrome p450 reductase N-terminal domain-like	0.3442	Inherited
Erythroid transcription factor GATA-1	0.3442	Inherited
Myosin rod fragments	0.3494	Inherited
Nuclear receptor ligand-binding domain	0.4808	Inherited
Nuclear receptor	0.4808	Inherited
L domain	0.5127	Inherited
HLH, helix-loop-helix DNA-binding domain	0.9499	Inherited
Ngr ectodomain-like	0.9821	Inherited
Homeodomain	1	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)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
MIR domain	0.00002161	Direct
IP3 receptor type 1 binding core, domain 2	0.0000269	Direct
Voltage-gated potassium channels	0.00092	Direct
Metal cation-transporting ATPase, ATP-binding domain N	0.001036	Inherited
SRF-like	0.001233	Inherited
WW domain	0.01321	Inherited
Transducin (alpha subunit), insertion domain	0.0158	Inherited
Inhibitor of apoptosis (IAP) repeat	0.01685	Inherited
Nucleotide cyclase	0.04293	Inherited
BPTI-like	0.0534	Inherited
Calcium ATPase, transduction domain A	0.0653	Inherited
Calcium ATPase, transmembrane domain M	0.0653	Inherited
E set domains	0.07114	Inherited
POZ domain	0.108	Inherited
Lipocalins	0.1686	Inherited
Flavoproteins	0.3389	Inherited
Myosin rod fragments	0.3448	Inherited
Riboflavin synthase domain-like	0.4208	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.4208	Inherited
Nuclear receptor ligand-binding domain	0.4781	Inherited
Family A G protein-coupled receptor-like	0.5055	Inherited
alpha-catenin/vinculin-like	0.6086	Inherited
dsRNA-binding domain-like	0.7054	Inherited
L domain-like	0.8292	Inherited
HLH, helix-loop-helix DNA-binding domain	0.9452	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)
100909,49899 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases	0	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.00001246	Direct
82109,82109 82109 - MIR domain 82109 - MIR domain	0.0000269	Direct
82109,100909 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2	0.0000269	Direct
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin	0.0007992	Direct
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0.001036	Inherited
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.004232	Inherited
47473,57850 47473 - EF-hand 57850 - RING/U-box	0.004232	Inherited
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.01143	Inherited
56784,81665 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0.08624	Inherited
90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments	0.15	Inherited
47473,47473 47473 - EF-hand 47473 - EF-hand	0.1521	Inherited
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.274	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.5085	Inherited
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.5085	Inherited
47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0.6086	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)
82109,100909,49899 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2 49899 - Concanavalin A-like lectins/glucanases	0	Direct
82109,82109,100909 82109 - MIR domain 82109 - MIR domain 100909 - IP3 receptor type 1 binding core, domain 2	0.0000269	Direct
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.0001876	Direct
90257,90257,90257 90257 - Myosin rod fragments 90257 - Myosin rod fragments 90257 - Myosin rod fragments	0.0001908	Direct
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.0007992	Direct
81660,56784,81665 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0.001036	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)	0.002138	Inherited
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.004232	Inherited
47473,47473,57850 47473 - EF-hand 47473 - EF-hand 57850 - RING/U-box	0.004232	Inherited
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.5085	Inherited
47220,47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0.6086	Inherited