Mammalian Phenotype (MP): embryonic lethality

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)
GroEL-intermediate domain like	0	Direct
Ribonuclease PH domain 2-like	0	Direct
ARM repeat	0.00007545	Direct
SMAD MH1 domain	0.001219	Inherited
GroEL apical domain-like	0.003636	Inherited
DNA clamp	0.003636	Inherited
HCP-like	0.003975	Inherited
ADC-like	0.01255	Inherited
dsRNA-binding domain-like	0.01619	Inherited
Subtilisin-like	0.03267	Inherited
SCOP hierarchy in SUPERFAMILY	0.2419	Inherited
BRCT domain	0.2455	Inherited
Cullin homology domain	0.416	Inherited
Zinc beta-ribbon	0.4983	Inherited
p53-like transcription factors	0.724	Inherited
Nucleic acid-binding proteins	0.724	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)
Chromo barrel domain	0	Direct
Ribonuclease PH domain 1-like	0	Direct
DNA ligase	0	Direct
Group II chaperonin (CCT, TRIC), apical domain	0	Direct
Fumble-like	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Ribonuclease PH domain 2-like	0	Direct
RecA protein-like (ATPase-domain)	0.00005436	Direct
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.0001639	Direct
Inhibitor of apoptosis (IAP) repeat	0.000584	Direct
SMAD MH1 domain	0.000717	Direct
SMAD domain	0.000717	Direct
SCF ubiquitin ligase complex WHB domain	0.00226	Inherited
Armadillo repeat	0.006316	Inherited
Proprotein convertase P-domain	0.008236	Inherited
Prohormone convertase 1 pro-domain	0.008236	Inherited
DNA polymerase I	0.008236	Inherited
C5 cytosine-specific DNA methylase, DCM	0.008428	Inherited
Subtilases	0.01329	Inherited
Tandem AAA-ATPase domain	0.02587	Inherited
T-box	0.1267	Inherited
Extracellular domain of cell surface receptors	0.2363	Inherited
Erythroid transcription factor GATA-1	0.2914	Inherited
Histone lysine methyltransferases	0.3516	Inherited
Cullin homology domain	0.359	Inherited
Ubiquitin carboxyl-terminal hydrolase, UCH	0.3974	Inherited
Linker histone H1/H5	0.4415	Inherited
N-acetyl transferase, NAT	0.6939	Inherited
Cell cycle transcription factor e2f-dp	0.7585	Inherited
Extended AAA-ATPase domain	0.8071	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)
Ribonuclease PH domain 2-like	0	Direct
GroEL-intermediate domain like	0	Direct
ARM repeat	0.00003607	Direct
SMAD MH1 domain	0.0006731	Direct
GroEL apical domain-like	0.002131	Inherited
DNA clamp	0.002131	Inherited
HCP-like	0.002343	Inherited
ADC-like	0.007962	Inherited
dsRNA-binding domain-like	0.01046	Inherited
Subtilisin-like	0.02235	Inherited
BRCT domain	0.2056	Inherited
Cullin homology domain	0.3689	Inherited
Zinc beta-ribbon	0.4505	Inherited
Nucleic acid-binding proteins	0.6844	Inherited
p53-like transcription factors	0.6844	Inherited
Acyl-CoA N-acyltransferases (Nat)	0.7511	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)
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0	Direct
54211,55666 54211 - Ribosomal protein S5 domain 2-like 55666 - Ribonuclease PH domain 2-like	0	Direct
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0.002131	Inherited
52113,52113 52113 - BRCT domain 52113 - BRCT domain	0.002343	Inherited
52743,49785 52743 - Subtilisin-like 49785 - Galactose-binding domain-like	0.007787	Inherited
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.01793	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.01793	Inherited
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.02061	Inherited
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like	0.02427	Inherited
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0.3689	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)
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0	Direct
54897,52743,49785 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like 49785 - Galactose-binding domain-like	0.007787	Inherited
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.01793	Inherited
54160,54160,52540 54160 - Chromo domain-like 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0.3689	Inherited
54160,52540,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.3689	Inherited