Mammalian Phenotype (MP): abnormal immune cell 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
STAT	0	Direct
Transcription factor STAT-4 N-domain	0	Direct
SH2 domain	0.00004457	Direct
Immunoglobulin	0.00005043	Direct
DEATH domain	0.0001575	Direct
SH3-domain	0.0001584	Direct
p53-like transcription factors	0.003053	Inherited
DBL homology domain (DH-domain)	0.01821	Inherited
Toll/Interleukin receptor TIR domain	0.03012	Inherited
TNF receptor-like	0.03303	Inherited
Caspase-like	0.05643	Inherited
MHC antigen-recognition domain	0.05687	Inherited
Flavoproteins	0.07605	Inherited
Interleukin 8-like chemokines	0.1007	Inherited
L30e-like	0.11	Inherited
Bcl-2 inhibitors of programmed cell death	0.138	Inherited
Cysteine-rich domain	0.1402	Inherited
Inhibitor of apoptosis (IAP) repeat	0.1845	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.2452	Inherited
4-helical cytokines	0.2622	Inherited
E set domains	0.2714	Inherited
Integrin domains	0.3076	Inherited
WWE domain	0.3268	Inherited
TNF-like	0.3357	Inherited
Integrin beta tail domain	0.4751	Inherited
Integrin alpha N-terminal domain	0.494	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.5647	Inherited
C-type lectin-like	0.5744	Inherited
SMAD/FHA domain	0.6202	Inherited
Family A G protein-coupled receptor-like	0.6552	Inherited
vWA-like	0.7931	Inherited
Complement control module/SCR domain	0.883	Inherited
L domain-like	0.9959	Inherited
EGF/Laminin	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)
Cysteine rich domain	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Proteasome subunits	0	Direct
STAT DNA-binding domain	0	Direct
Transcription factor STAT-4 N-domain	0	Direct
STAT	0	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.0000006184	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.00001721	Direct
SH2 domain	0.0000214	Direct
Pyrin domain, PYD	0.00007398	Direct
SH3-domain	0.00007998	Direct
Inhibitor of apoptosis (IAP) repeat	0.000333	Direct
28-residue LRR	0.0007249	Direct
Pleckstrin-homology domain (PH domain)	0.002478	Inherited
C1 set domains (antibody constant domain-like)	0.005265	Inherited
Cytochrome p450 reductase N-terminal domain-like	0.005909	Inherited
V set domains (antibody variable domain-like)	0.006656	Inherited
DBL homology domain (DH-domain)	0.01583	Inherited
NADPH-cytochrome p450 reductase-like	0.01828	Inherited
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.01828	Inherited
Caspase recruitment domain, CARD	0.02109	Inherited
Toll/Interleukin receptor TIR domain	0.02726	Inherited
MHC antigen-recognition domain	0.04146	Inherited
TNF receptor-like	0.04146	Inherited
Caspase catalytic domain	0.05747	Inherited
I set domains	0.0664	Inherited
Interleukin 8-like chemokines	0.07711	Inherited
DEATH domain, DD	0.07711	Inherited
ets domain	0.09077	Inherited
Short-chain cytokines	0.09641	Inherited
Bcl-2 inhibitors of programmed cell death	0.1104	Inherited
PLC-like (P variant)	0.1192	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.2107	Inherited
C-type lectin domain	0.2557	Inherited
Integrin domains	0.2663	Inherited
Interferon regulatory factor	0.2694	Inherited
WWE domain	0.2857	Inherited
TNF-like	0.2925	Inherited
Integrin alpha N-terminal domain	0.3676	Inherited
Rhodopsin-like	0.4192	Inherited
FHA domain	0.4223	Inherited
Integrin beta tail domain	0.4316	Inherited
Interferon regulatory factor 3 (IRF3), transactivation domain	0.4316	Inherited
Integrin beta EGF-like domains	0.4316	Inherited
Interleukin 17F, IL-17F	0.5365	Inherited
Integrin A (or I) domain	0.644	Inherited
Complement control module/SCR domain	0.8589	Inherited
EGF-type module	0.983	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)
Transcription factor STAT-4 N-domain	0	Direct
STAT	0	Direct
Nitric oxide (NO) synthase oxygenase domain	0	Direct
SH2 domain	0.00002084	Direct
Immunoglobulin	0.00002369	Direct
DEATH domain	0.00007874	Direct
SH3-domain	0.00007921	Direct
p53-like transcription factors	0.001772	Inherited
DBL homology domain (DH-domain)	0.01188	Inherited
Toll/Interleukin receptor TIR domain	0.02048	Inherited
TNF receptor-like	0.0226	Inherited
Caspase-like	0.04034	Inherited
MHC antigen-recognition domain	0.04069	Inherited
Flavoproteins	0.05598	Inherited
Interleukin 8-like chemokines	0.07608	Inherited
L30e-like	0.08407	Inherited
Bcl-2 inhibitors of programmed cell death	0.1083	Inherited
Cysteine-rich domain	0.11	Inherited
RNI-like	0.1175	Inherited
Inhibitor of apoptosis (IAP) repeat	0.1493	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.2054	Inherited
4-helical cytokines	0.221	Inherited
E set domains	0.2298	Inherited
Integrin domains	0.2639	Inherited
WWE domain	0.2824	Inherited
TNF-like	0.2907	Inherited
Integrin beta tail domain	0.4274	Inherited
Integrin alpha N-terminal domain	0.4463	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.5182	Inherited
C-type lectin-like	0.528	Inherited
SMAD/FHA domain	0.5753	Inherited
Family A G protein-coupled receptor-like	0.612	Inherited
vWA-like	0.7578	Inherited
Transducin (alpha subunit), insertion domain	0.7688	Inherited
Complement control module/SCR domain	0.8548	Inherited
L domain-like	0.9818	Inherited
EGF/Laminin	0.9951	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)
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0	Direct
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain)	0	Direct
48366,47473 48366 - Ras GEF 47473 - EF-hand	0	Direct
57440,56436 57440 - Kringle-like 56436 - C-type lectin-like	0	Direct
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0	Direct
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0	Direct
50370,57440 50370 - Ricin B-like lectins 57440 - Kringle-like	0	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.0000003951	Direct
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.0002688	Direct
47986,52540 47986 - DEATH domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.0003014	Direct
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.004309	Inherited
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat	0.005071	Inherited
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.0122	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.01788	Inherited
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.02056	Inherited
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.0226	Inherited
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0.03312	Inherited
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.09466	Inherited
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.1083	Inherited
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.1493	Inherited
57889,57889 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0.1493	Inherited
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0.1493	Inherited
53300,69318 53300 - vWA-like 69318 - Integrin alpha N-terminal domain	0.2054	Inherited
53300,69179 53300 - vWA-like 69179 - Integrin domains	0.2054	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.2181	Inherited
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.2824	Inherited
69179,69179 69179 - Integrin domains 69179 - Integrin domains	0.3641	Inherited
69318,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0.3641	Inherited
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases	0.4274	Inherited
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0.4274	Inherited
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.6227	Inherited
57535,57535 57535 - Complement control module/SCR domain 57535 - Complement control module/SCR domain	0.8043	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)
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0	Direct
50044,55550,50044 50044 - SH3-domain 55550 - SH2 domain 50044 - SH3-domain	0	Direct
48366,47473,57889 48366 - Ras GEF 47473 - EF-hand 57889 - Cysteine-rich domain	0	Direct
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0	Direct
57440,56436,56436 57440 - Kringle-like 56436 - C-type lectin-like 56436 - C-type lectin-like	0	Direct
50370,57440,56436 50370 - Ricin B-like lectins 57440 - Kringle-like 56436 - C-type lectin-like	0	Direct
50729,50044,55550 50729 - PH domain-like 50044 - SH3-domain 55550 - SH2 domain	0	Direct
57850,49599,49599 57850 - RING/U-box 49599 - TRAF domain-like 49599 - TRAF domain-like	0	Direct
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.005071	Inherited
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.005071	Inherited
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.02056	Inherited
49265,49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III 49265 - Fibronectin type III	0.02698	Inherited
53300,69318,69179 53300 - vWA-like 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0.2054	Inherited
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.2054	Inherited
57440,57440,50494 57440 - Kringle-like 57440 - Kringle-like 50494 - Trypsin-like serine proteases	0.2824	Inherited
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.2824	Inherited
69318,69179,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains 69179 - Integrin domains	0.3641	Inherited
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0.4274	Inherited
69179,69179,69179 69179 - Integrin domains 69179 - Integrin domains 69179 - Integrin domains	0.4409	Inherited