Mammalian Phenotype (MP): lethality during fetal growth through weaning

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

Jump to [ Top · Hierarchy ]

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
ATP-dependent DNA ligase DNA-binding domain	0	Direct
A heparin-binding domain	0	Direct
SRF-like	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
p53 tetramerization domain	0	Direct
DNA ligase/mRNA capping enzyme, catalytic domain	0	Direct
Amyloid beta a4 protein copper binding domain (domain 2)	0	Direct
Lamin A/C globular tail domain	0	Direct
CAPPD, an extracellular domain of amyloid beta A4 protein	0	Direct
Homeodomain-like	0.0000000000005699	Direct
HLH, helix-loop-helix DNA-binding domain	0.000121	Direct
EGF/Laminin	0.0002139	Direct
GAT-like domain	0.003806	Inherited
Protein kinase-like (PK-like)	0.003857	Inherited
Growth factor receptor domain	0.005917	Inherited
L27 domain	0.05594	Inherited
p53-like transcription factors	0.0582	Inherited
E2F-DP heterodimerization region	0.09941	Inherited
TB module/8-cys domain	0.1395	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

Jump to [ Top · Hierarchy ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Paired domain	0	Direct
Lamin A/C globular tail domain	0	Direct
CAPPD, an extracellular domain of amyloid beta A4 protein	0	Direct
A heparin-binding domain	0	Direct
DNA ligase/mRNA capping enzyme postcatalytic domain	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
p53 DNA-binding domain-like	0	Direct
RUNT domain	0	Direct
Amyloid beta a4 protein copper binding domain (domain 2)	0	Direct
Neurotrophin	0	Direct
L domain	0	Direct
ATP-dependent DNA ligase catalytic domain	0	Direct
p53 tetramerization domain	0	Direct
E2F dimerization segment	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
SRF-like	0	Direct
Homeodomain	0.0000000000006016	Direct
Forkhead DNA-binding domain	0.00002358	Direct
HLH, helix-loop-helix DNA-binding domain	0.0002201	Direct
Erythroid transcription factor GATA-1	0.0003513	Direct
Growth factor receptor domain	0.002157	Inherited
Protein kinases, catalytic subunit	0.003593	Inherited
Laminin G-like module	0.01737	Inherited
GAT domain	0.02343	Inherited
HMA, heavy metal-associated domain	0.02343	Inherited
Cell cycle transcription factor e2f-dp	0.04485	Inherited
L27 domain	0.05041	Inherited
Extracellular domain of cell surface receptors	0.09147	Inherited
Blood coagulation inhibitor (disintegrin)	0.1142	Inherited
TB module/8-cys domain	0.1293	Inherited
Enabled/VASP homology 1 domain (EVH1 domain)	0.2043	Inherited
Adenosine/AMP deaminase	0.2571	Inherited
gamma-adaptin C-terminal appendage domain-like	0.2571	Inherited
Pointed domain	0.3016	Inherited
ZZ domain	0.3016	Inherited
DNA replication initiator (cdc21/cdc54) N-terminal domain	0.3016	Inherited
ets domain	0.3787	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

Jump to [ Top · Hierarchy ]

Supra-domain (Single)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
ATP-dependent DNA ligase DNA-binding domain	0	Direct
A heparin-binding domain	0	Direct
Amyloid beta a4 protein copper binding domain (domain 2)	0	Direct
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
SRF-like	0	Direct
DNA ligase/mRNA capping enzyme, catalytic domain	0	Direct
Lamin A/C globular tail domain	0	Direct
p53 tetramerization domain	0	Direct
CAPPD, an extracellular domain of amyloid beta A4 protein	0	Direct
Homeodomain-like	0.0000000000002065	Direct
HLH, helix-loop-helix DNA-binding domain	0.00005948	Direct
EGF/Laminin	0.0001086	Direct
GAT-like domain	0.002234	Inherited
Protein kinase-like (PK-like)	0.002267	Inherited
Growth factor receptor domain	0.003569	Inherited
Orange domain-like	0.008684	Inherited
HMA, heavy metal-associated domain	0.01922	Inherited
L27 domain	0.03995	Inherited
p53-like transcription factors	0.04173	Inherited
E2F-DP heterodimerization region	0.07497	Inherited
Blood coagulation inhibitor (disintegrin)	0.08879	Inherited
TB module/8-cys domain	0.1094	Inherited
Inhibitor of apoptosis (IAP) repeat	0.1588	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

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

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
52058,49265 52058 - L domain-like 49265 - Fibronectin type III	0	Direct
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain	0	Direct
50729,50156 50729 - PH domain-like 50156 - PDZ domain-like	0	Direct
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
56491,89811 56491 - A heparin-binding domain 89811 - Amyloid beta a4 protein copper binding domain (domain 2)	0	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
117018,56091 117018 - ATP-dependent DNA ligase DNA-binding domain 56091 - DNA ligase/mRNA capping enzyme, catalytic domain	0	Direct
56091,50249 56091 - DNA ligase/mRNA capping enzyme, catalytic domain 50249 - Nucleic acid-binding proteins	0	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
49562,51045 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 51045 - WW domain	0	Direct
64593,74853 64593 - Intermediate filament protein, coiled coil region 74853 - Lamin A/C globular tail domain	0	Direct
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	Direct
48464,89009 48464 - ENTH/VHS domain 89009 - GAT-like domain	0.002234	Inherited
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.008684	Inherited
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.01573	Inherited
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0.01922	Inherited
53300,69179 53300 - vWA-like 69179 - Integrin domains	0.04779	Inherited
101288,50156 101288 - L27 domain 50156 - PDZ domain-like	0.04779	Inherited
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.05422	Inherited
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0.07497	Inherited
55486,57552 55486 - Metalloproteases ("zincins"), catalytic domain 57552 - Blood coagulation inhibitor (disintegrin)	0.08879	Inherited
57184,63825 57184 - Growth factor receptor domain 63825 - YWTD domain	0.1094	Inherited
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain	0.1094	Inherited
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain	0.1094	Inherited
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0.1588	Inherited
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0.1588	Inherited
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0.1588	Inherited
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.264	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

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

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
100895,100895,100895 100895 - Kazal-type serine protease inhibitors 100895 - Kazal-type serine protease inhibitors 100895 - Kazal-type serine protease inhibitors	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
54928,54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0	Direct
50729,50156,50156 50729 - PH domain-like 50156 - PDZ domain-like 50156 - PDZ domain-like	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
52058,49265,49265 52058 - L domain-like 49265 - Fibronectin type III 49265 - Fibronectin type III	0	Direct
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0	Direct
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
117018,56091,50249 117018 - ATP-dependent DNA ligase DNA-binding domain 56091 - DNA ligase/mRNA capping enzyme, catalytic domain 50249 - Nucleic acid-binding proteins	0	Direct
57184,52058,49265 57184 - Growth factor receptor domain 52058 - L domain-like 49265 - Fibronectin type III	0	Direct
49265,48726,49265 49265 - Fibronectin type III 48726 - Immunoglobulin 49265 - Fibronectin type III	0	Direct
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0.0001849	Direct
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.002234	Inherited
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.00667	Inherited
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0.00667	Inherited
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.008684	Inherited
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.05422	Inherited
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.05665	Inherited
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain	0.1094	Inherited
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain	0.1094	Inherited
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.1588	Inherited
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0.2299	Inherited