Mammalian Phenotype (MP): altered susceptibility to infection

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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).

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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 response to infection [MP:0005025] <2> (18|31) (21|17|5)

0: altered susceptibility to infection [MP:0001793] <8> (18|31) (21|17|5)

- 1: decreased susceptibility to infection [MP:0002409] <6> (1|4) (1|1|0)

- 1: increased susceptibility to infection [MP:0002406] <6> (11|19) (12|11|4)

- 1: altered susceptibility to bacterial infection [MP:0020186] <2> (6|14) (7|7|2)

- 1: altered susceptibility to fungal infection [MP:0020183] <2> (0|0) (0|0|0)

- 1: altered susceptibility to infection induced morbidity/mortality [MP:0009785] <2> (2|2) (2|1|0)

- 1: altered susceptibility to parasitic infection [MP:0020184] <2> (0|1) (0|1|0)

- 1: altered susceptibility to prion infection [MP:0020187] <2> (0|0) (0|0|0)

- 1: altered susceptibility to viral infection [MP:0020185] <2> (1|3) (1|1|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Anaphylotoxins (complement system)	0	Direct
DEATH domain	0.000000000005547	Direct
C-type lectin-like	0.0000000001327	Direct
4-helical cytokines	0.0000000003172	Direct
Toll/Interleukin receptor TIR domain	0.0000000008521	Direct
PGBD-like	0.00002415	Direct
MHC antigen-recognition domain	0.0003264	Direct
Triple coiled coil domain of C-type lectins	0.0004326	Direct
Hemopexin-like domain	0.000666	Direct
TNF receptor-like	0.002692	Inherited
RNI-like	0.003552	Inherited
Alpha-macroglobulin receptor domain	0.006198	Inherited
dsRNA-binding domain-like	0.02569	Inherited
Caspase-like	0.03526	Inherited
p53-like transcription factors	0.5326	Inherited
Immunoglobulin	0.5771	Inherited
STAT	0.8236	Inherited
Transcription factor STAT-4 N-domain	0.8236	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Anaphylotoxins (complement system)	0	Direct
C-type lectin domain	0.000000000001854	Direct
Toll/Interleukin receptor TIR domain	0.000000006235	Direct
Interferon regulatory factor 3 (IRF3), transactivation domain	0.000000198	Direct
Caspase recruitment domain, CARD	0.000005262	Direct
Short-chain cytokines	0.000009376	Direct
MMP N-terminal domain	0.00001749	Direct
DEATH domain, DD	0.00002082	Direct
Interleukin 17F, IL-17F	0.00002774	Direct
Matrix metalloproteases, catalytic domain	0.00002922	Direct
C1 set domains (antibody constant domain-like)	0.00004676	Direct
Interferons/interleukin-10 (IL-10)	0.0001087	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.0002121	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.0002273	Direct
MHC antigen-recognition domain	0.00024	Direct
Triple coiled coil domain of C-type lectins	0.0002841	Direct
Hemopexin-like domain	0.0005	Direct
TNF receptor-like	0.0005267	Direct
Eukaryotic proteases	0.0006595	Direct
Interleukin-1 (IL-1)	0.001034	Inherited
Netrin-like domain (NTR/C345C module)	0.001034	Inherited
Long-chain cytokines	0.001694	Inherited
Complement components	0.004591	Inherited
Alpha-macroglobulin receptor domain	0.004591	Inherited
Fibronectin type II module	0.01621	Inherited
Caspase catalytic domain	0.02192	Inherited
Double-stranded RNA-binding domain (dsRBD)	0.03587	Inherited
Interferon regulatory factor	0.7029	Inherited
STAT DNA-binding domain	0.8057	Inherited
Transcription factor STAT-4 N-domain	0.8057	Inherited
STAT	0.8057	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)
Anaphylotoxins (complement system)	0	Direct
DEATH domain	0.000000000002004	Direct
C-type lectin-like	0.00000000004853	Direct
4-helical cytokines	0.0000000001162	Direct
Toll/Interleukin receptor TIR domain	0.0000000003153	Direct
PGBD-like	0.00001099	Direct
MHC antigen-recognition domain	0.000169	Direct
Triple coiled coil domain of C-type lectins	0.0002269	Direct
Hemopexin-like domain	0.0003563	Direct
TNF-like	0.0007316	Direct
Trypsin-like serine proteases	0.0008742	Direct
TNF receptor-like	0.001552	Inherited
RNI-like	0.002081	Inherited
Alpha-macroglobulin receptor domain	0.003763	Inherited
Integrin alpha N-terminal domain	0.01426	Inherited
dsRNA-binding domain-like	0.01721	Inherited
Caspase-like	0.02427	Inherited
p53-like transcription factors	0.4855	Inherited
Immunoglobulin	0.5307	Inherited
STAT	0.7904	Inherited
Transcription factor STAT-4 N-domain	0.7904	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49410,50242 49410 - Alpha-macroglobulin receptor domain 50242 - TIMP-like	0	Direct
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.0000002268	Direct
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.000005356	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.00001099	Direct
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.00004152	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.0001691	Direct
57944,56436 57944 - Triple coiled coil domain of C-type lectins 56436 - C-type lectin-like	0.0002269	Direct
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.0005392	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.0006565	Direct
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.001982	Inherited
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.002642	Inherited
47986,52540 47986 - DEATH domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.006277	Inherited
53300,69318 53300 - vWA-like 69318 - Integrin alpha N-terminal domain	0.006277	Inherited
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0.009526	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.7904	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.7904	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.7904	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.000169	Direct
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.001888	Inherited
53300,69318,69179 53300 - vWA-like 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0.006277	Inherited
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.7904	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.7904	Inherited

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

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Mammalian Phenotype (MP): altered susceptibility to infection

Superfamily

Family

Supra-domain (including individual superfamily)