Mammalian Phenotype (MP): abnormal professional antigen presenting cell physiology

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Phenotype Ontology
Like Gene Ontology (GO), phenotypy 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. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
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)
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)
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 (YP)
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)
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)
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)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
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 (AP)
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 (EC)
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.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
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).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Root: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)

Shortest distance to current term (+ for parents, - for children) MP term [MP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + 4: mammalian phenotype [MP:0000001] <29>

+ + + 3: immune system phenotype [MP:0005387] <2> (76|114) (86|66|35)

+ + 2: abnormal immune system physiology [MP:0001790] <16> (59|84) (66|49|28)

+ 1: abnormal immune cell physiology [MP:0001819] <3> (35|48) (37|33|21)

+ 1: abnormal adaptive immunity [MP:0002420] <8> (36|48) (38|33|21)

+ 1: abnormal cell-mediated immunity [MP:0002421] <3> (35|48) (37|33|21)

0: abnormal professional antigen presenting cell physiology [MP:0002452] <3> (25|32) (26|19|12)

- 1: abnormal macrophage physiology [MP:0002451] <10> (7|6) (8|4|2)

- 1: abnormal B cell physiology [MP:0002459] <9> (19|27) (20|16|10)

- 1: abnormal dendritic cell physiology [MP:0002376] <5> (2|2) (2|0|0)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
DEATH domain	0.01516	Inherited
WWE domain	0.02898	Inherited
Flavoproteins	0.02898	Inherited
4-helical cytokines	0.02977	Inherited
Toll/Interleukin receptor TIR domain	0.02977	Inherited
L30e-like	0.04409	Inherited
E set domains	0.1406	Inherited
TNF receptor-like	0.2002	Inherited
TNF-like	0.2002	Inherited
Bcl-2 inhibitors of programmed cell death	0.2146	Inherited
SMAD/FHA domain	0.2388	Inherited
SH2 domain	0.245	Inherited
L domain-like	0.2853	Inherited
EGF/Laminin	0.3606	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.3614	Inherited
p53-like transcription factors	0.4805	Inherited
Caspase-like	0.5467	Inherited
DBL homology domain (DH-domain)	0.5706	Inherited
Inhibitor of apoptosis (IAP) repeat	0.6231	Inherited
MHC antigen-recognition domain	0.698	Inherited
STAT	0.7132	Inherited
Transcription factor STAT-4 N-domain	0.7132	Inherited
Family A G protein-coupled receptor-like	0.7506	Inherited
SH3-domain	0.8118	Inherited

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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
Short-chain cytokines	0.0000001168	Direct
Cytochrome p450 reductase N-terminal domain-like	0.001762	Inherited
NADPH-cytochrome p450 reductase-like	0.005943	Inherited
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.005943	Inherited
Interleukin 17F, IL-17F	0.005943	Inherited
WWE domain	0.01292	Inherited
ets domain	0.01762	Inherited
Toll/Interleukin receptor TIR domain	0.03061	Inherited
I set domains	0.03974	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.05995	Inherited
Rel/Dorsal transcription factors, DNA-binding domain	0.08021	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1418	Inherited
TNF-like	0.1786	Inherited
C1 set domains (antibody constant domain-like)	0.1786	Inherited
Bcl-2 inhibitors of programmed cell death	0.1881	Inherited
FHA domain	0.1909	Inherited
DEATH domain, DD	0.2173	Inherited
SH2 domain	0.234	Inherited
TNF receptor-like	0.2621	Inherited
PLC-like (P variant)	0.2983	Inherited
V set domains (antibody variable domain-like)	0.3041	Inherited
Proteasome subunits	0.3301	Inherited
DBL homology domain (DH-domain)	0.5488	Inherited
Inhibitor of apoptosis (IAP) repeat	0.5954	Inherited
Caspase catalytic domain	0.6036	Inherited
Pleckstrin-homology domain (PH domain)	0.6307	Inherited
MHC antigen-recognition domain	0.6782	Inherited
STAT DNA-binding domain	0.6907	Inherited
Transcription factor STAT-4 N-domain	0.6907	Inherited
STAT	0.6907	Inherited
SH3-domain	0.8093	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
DEATH domain	0.009741	Inherited
WWE domain	0.01963	Inherited
Flavoproteins	0.01963	Inherited
Toll/Interleukin receptor TIR domain	0.02023	Inherited
4-helical cytokines	0.02023	Inherited
L30e-like	0.03084	Inherited
RNI-like	0.05855	Inherited
E set domains	0.1104	Inherited
TNF receptor-like	0.1634	Inherited
TNF-like	0.1634	Inherited
Bcl-2 inhibitors of programmed cell death	0.1768	Inherited
SMAD/FHA domain	0.1993	Inherited
SH2 domain	0.2051	Inherited
L domain-like	0.2428	Inherited
EGF/Laminin	0.3148	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.3157	Inherited
p53-like transcription factors	0.4328	Inherited
Caspase-like	0.4999	Inherited
DBL homology domain (DH-domain)	0.5243	Inherited
Inhibitor of apoptosis (IAP) repeat	0.5782	Inherited
MHC antigen-recognition domain	0.657	Inherited
STAT	0.6732	Inherited
Transcription factor STAT-4 N-domain	0.6732	Inherited
Family A G protein-coupled receptor-like	0.7124	Inherited
SH3-domain	0.7777	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain)	0	Direct
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat	0.001458	Inherited
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.00497	Inherited
57440,50494 57440 - Kringle-like 50494 - Trypsin-like serine proteases	0.005136	Inherited
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0.01097	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.02436	Inherited
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.05855	Inherited
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.07302	Inherited
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.1071	Inherited
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.1993	Inherited
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.2359	Inherited
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.2359	Inherited
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0.2359	Inherited
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.3546	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.3838	Inherited
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.4757	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.6732	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.6732	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.6732	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
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
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.001458	Inherited
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.001458	Inherited
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0.00497	Inherited
57440,57440,50494 57440 - Kringle-like 57440 - Kringle-like 50494 - Trypsin-like serine proteases	0.00497	Inherited
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.1577	Inherited
49265,49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III 49265 - Fibronectin type III	0.1768	Inherited
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.3157	Inherited
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.6732	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.6732	Inherited

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Mammalian Phenotype (MP): abnormal professional antigen presenting cell physiology

Superfamily

Family

Supra-domain (including individual superfamily)