Mammalian Phenotype (MP): respiratory system phenotype

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
p53 tetramerization domain	0	Direct
Lamin A/C globular tail domain	0	Direct
p53-like transcription factors	0.000005384	Direct
Homeodomain-like	0.00001261	Direct
FnI-like domain	0.00002228	Direct
Protein kinase-like (PK-like)	0.00005029	Direct
4-helical cytokines	0.0001307	Direct
EGF/Laminin	0.0001315	Direct
Growth factor receptor domain	0.001317	Inherited
Notch domain	0.001601	Inherited
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0.006689	Inherited
L27 domain	0.008317	Inherited
Kringle-like	0.009211	Inherited
HLH, helix-loop-helix DNA-binding domain	0.009806	Inherited
Snake toxin-like	0.0109	Inherited
E2F-DP heterodimerization region	0.01321	Inherited
Flavoproteins	0.01321	Inherited
Riboflavin synthase domain-like	0.02348	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.02348	Inherited
PGBD-like	0.02471	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.04663	Inherited
Hemopexin-like domain	0.0536	Inherited
Family A G protein-coupled receptor-like	0.06488	Inherited
TNF receptor-like	0.1006	Inherited
Integrin domains	0.1117	Inherited
DEATH domain	0.1187	Inherited
Nuclear receptor ligand-binding domain	0.1579	Inherited
Toll/Interleukin receptor TIR domain	0.162	Inherited
Voltage-gated potassium channels	0.3484	Inherited
Integrin alpha N-terminal domain	0.4597	Inherited
Trypsin-like serine proteases	0.8436	Inherited
PH domain-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)
Lamin A/C globular tail domain	0	Direct
p53 DNA-binding domain-like	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
RUNT domain	0	Direct
p53 tetramerization domain	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Cytochrome p450 reductase N-terminal domain-like	0	Direct
Homeodomain	0.000001762	Direct
Extracellular domain of cell surface receptors	0.00001435	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.00001435	Direct
Short-chain cytokines	0.00004235	Direct
VWC domain	0.00004235	Direct
Forkhead DNA-binding domain	0.00005248	Direct
L domain	0.00005335	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.0001094	Direct
Protein kinases, catalytic subunit	0.0001793	Direct
Growth factor receptor domain	0.0003846	Direct
Cell cycle transcription factor e2f-dp	0.00086	Direct
Notch domain	0.001149	Inherited
NADPH-cytochrome p450 reductase-like	0.001149	Inherited
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.001149	Inherited
EGF-type module	0.002958	Inherited
Hypoxia-inducible factor Hif2a, C-terminal domain	0.004344	Inherited
E2F dimerization segment	0.004376	Inherited
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0.00498	Inherited
Phenylalanine metabolism regulatory domain	0.00498	Inherited
L27 domain	0.006601	Inherited
HLH, helix-loop-helix DNA-binding domain	0.01097	Inherited
Kringle modules	0.01771	Inherited
Erythroid transcription factor GATA-1	0.01976	Inherited
MMP N-terminal domain	0.02141	Inherited
Matrix metalloproteases, catalytic domain	0.0287	Inherited
Interferons/interleukin-10 (IL-10)	0.03241	Inherited
TNF receptor-like	0.03479	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.04179	Inherited
Rhodopsin-like	0.04503	Inherited
Hemopexin-like domain	0.04811	Inherited
Integrin domains	0.1048	Inherited
Nuclear receptor	0.128	Inherited
Toll/Interleukin receptor TIR domain	0.131	Inherited
Nuclear receptor ligand-binding domain	0.1571	Inherited
DEATH domain, DD	0.1614	Inherited
LIM domain	0.3282	Inherited
Integrin alpha N-terminal domain	0.3473	Inherited
Eukaryotic proteases	0.788	Inherited
Phosphotyrosine-binding domain (PTB)	0.8393	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
p53 tetramerization domain	0	Direct
Lamin A/C globular tail domain	0	Direct
p53-like transcription factors	0.000002303	Direct
Homeodomain-like	0.000005567	Direct
FnI-like domain	0.00001007	Direct
Protein kinase-like (PK-like)	0.0000236	Direct
4-helical cytokines	0.00006474	Direct
EGF/Laminin	0.00006517	Direct
Growth factor receptor domain	0.0007311	Direct
Notch domain	0.0008991	Direct
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0.004083	Inherited
FAS1 domain	0.004083	Inherited
L27 domain	0.005136	Inherited
Kringle-like	0.005716	Inherited
HLH, helix-loop-helix DNA-binding domain	0.006119	Inherited
Snake toxin-like	0.006856	Inherited
E2F-DP heterodimerization region	0.008409	Inherited
Flavoproteins	0.008409	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.01561	Inherited
Riboflavin synthase domain-like	0.01561	Inherited
PGBD-like	0.01649	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.03283	Inherited
Hemopexin-like domain	0.03808	Inherited
Family A G protein-coupled receptor-like	0.04709	Inherited
TNF receptor-like	0.07593	Inherited
Integrin domains	0.0855	Inherited
DEATH domain	0.09142	Inherited
Nuclear receptor ligand-binding domain	0.1257	Inherited
Toll/Interleukin receptor TIR domain	0.1292	Inherited
Cyclin-like	0.1942	Inherited
"Winged helix" DNA-binding domain	0.2071	Inherited
Voltage-gated potassium channels	0.3031	Inherited
Integrin alpha N-terminal domain	0.412	Inherited
Trypsin-like serine proteases	0.812	Inherited
PH domain-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)
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
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.000008918	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.00003703	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.00003703	Direct
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.002385	Inherited
57184,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.003332	Inherited
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0.003478	Inherited
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0.004083	Inherited
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0.004083	Inherited
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain	0.004083	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.006853	Inherited
101288,50156 101288 - L27 domain 50156 - PDZ domain-like	0.008409	Inherited
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0.008409	Inherited
57603,57603 57603 - FnI-like domain 57603 - FnI-like domain	0.008409	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.008447	Inherited
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0.01167	Inherited
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.01167	Inherited
57184,49899 57184 - Growth factor receptor domain 49899 - Concanavalin A-like lectins/glucanases	0.01298	Inherited
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases	0.01612	Inherited
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.01649	Inherited
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.02295	Inherited
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.02391	Inherited
55785,55785 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0.02697	Inherited
52799,49562 52799 - (Phosphotyrosine protein) phosphatases II 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0.02729	Inherited
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.1374	Inherited
69318,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0.2446	Inherited
69179,69179 69179 - Integrin domains 69179 - Integrin domains	0.2446	Inherited
50729,50729 50729 - PH domain-like 50729 - PH domain-like	0.6098	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)
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.00003703	Direct
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.0004229	Direct
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.001805	Inherited
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.003478	Inherited
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.008409	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.009039	Inherited
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.01298	Inherited
47459,55785,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain) 55785 - PYP-like sensor domain (PAS domain)	0.01612	Inherited
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain	0.02729	Inherited
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.05816	Inherited
69179,69179,69179 69179 - Integrin domains 69179 - Integrin domains 69179 - Integrin domains	0.1829	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)	0.2179	Inherited
69318,69179,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains 69179 - Integrin domains	0.2446	Inherited
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.5795	Inherited