Mammalian Phenotype (MP): abnormal cytokine secretion

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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 immune serum protein physiology [MP:0002723] <4> (25|40) (32|24|12)

0: abnormal cytokine secretion [MP:0003009] <4> (17|33) (23|19|8)

- 1: abnormal interleukin secretion [MP:0008568] <19> (13|26) (17|15|7)

- 1: abnormal interferon secretion [MP:0008555] <3> (9|17) (11|11|3)

- 1: abnormal tumor necrosis factor secretion [MP:0008556] <2> (2|4) (4|3|1)

- 1: abnormal chemokine secretion [MP:0008722] (1|1) (1|0|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
N-acetylmuramoyl-L-alanine amidase-like	0	Direct
STAT	0.0000009726	Direct
Transcription factor STAT-4 N-domain	0.0000009726	Direct
Toll/Interleukin receptor TIR domain	0.0007634	Direct
DEATH domain	0.002032	Inherited
Transducin (alpha subunit), insertion domain	0.006707	Inherited
RNI-like	0.02169	Inherited
SH2 domain	0.04005	Inherited
SH3-domain	0.1784	Inherited
Caspase-like	0.2156	Inherited
4-helical cytokines	0.2643	Inherited
SMAD/FHA domain	0.3561	Inherited
DBL homology domain (DH-domain)	0.3561	Inherited
TNF receptor-like	0.4243	Inherited
MHC antigen-recognition domain	0.5208	Inherited
L domain-like	0.5454	Inherited
TNF-like	0.6144	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Interleukin 17F, IL-17F	0	Direct
N-acetylmuramoyl-L-alanine amidase-like	0	Direct
Caspase recruitment domain, CARD	0.00000009002	Direct
STAT DNA-binding domain	0.0000006262	Direct
Transcription factor STAT-4 N-domain	0.0000006262	Direct
STAT	0.0000006262	Direct
Interferons/interleukin-10 (IL-10)	0.00001471	Direct
Interleukin-1 (IL-1)	0.0000599	Direct
Toll/Interleukin receptor TIR domain	0.0007526	Direct
Notch domain	0.001817	Inherited
Transducin (alpha subunit), insertion domain	0.00521	Inherited
DEATH domain, DD	0.01118	Inherited
SH2 domain	0.03361	Inherited
Cell cycle control phosphatase, catalytic domain	0.03483	Inherited
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.04727	Inherited
Rel/Dorsal transcription factors, DNA-binding domain	0.06711	Inherited
Interferon regulatory factor 3 (IRF3), transactivation domain	0.1337	Inherited
Pyrin domain, PYD	0.1337	Inherited
SH3-domain	0.1615	Inherited
28-residue LRR	0.1825	Inherited
V set domains (antibody variable domain-like)	0.2077	Inherited
Interferon regulatory factor	0.2381	Inherited
Caspase catalytic domain	0.2627	Inherited
RING finger domain, C3HC4	0.2736	Inherited
EF-hand modules in multidomain proteins	0.3097	Inherited
DBL homology domain (DH-domain)	0.3275	Inherited
TNF receptor-like	0.3353	Inherited
PLC-like (P variant)	0.3378	Inherited
C1 set domains (antibody constant domain-like)	0.4037	Inherited
MHC antigen-recognition domain	0.4914	Inherited
TNF-like	0.5906	Inherited
Pleckstrin-homology domain (PH domain)	0.8625	Inherited
Short-chain cytokines	0.9165	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)
N-acetylmuramoyl-L-alanine amidase-like	0	Direct
STAT	0.0000003962	Direct
Transcription factor STAT-4 N-domain	0.0000003962	Direct
Toll/Interleukin receptor TIR domain	0.0004106	Direct
DEATH domain	0.001156	Inherited
Notch domain	0.001485	Inherited
Transducin (alpha subunit), insertion domain	0.004095	Inherited
RNI-like	0.01432	Inherited
SH2 domain	0.02782	Inherited
SH3-domain	0.1436	Inherited
Caspase-like	0.1777	Inherited
Rhodanese/Cell cycle control phosphatase	0.1777	Inherited
4-helical cytokines	0.2229	Inherited
Cystine-knot cytokines	0.3009	Inherited
SMAD/FHA domain	0.3106	Inherited
DBL homology domain (DH-domain)	0.3106	Inherited
TNF receptor-like	0.3775	Inherited
MHC antigen-recognition domain	0.4733	Inherited
L domain-like	0.4986	Inherited
RING/U-box	0.5445	Inherited
TNF-like	0.5692	Inherited
PH domain-like	0.6936	Inherited
"Winged helix" DNA-binding domain	0.7625	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
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.0000003962	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.0000003962	Direct
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.0000003962	Direct
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.0001947	Direct
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0.0004153	Direct
55550,158235 55550 - SH2 domain 158235 - SOCS box-like	0.0005576	Direct
52821,52799 52821 - Rhodanese/Cell cycle control phosphatase 52799 - (Phosphotyrosine protein) phosphatases II	0.002188	Inherited
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.01503	Inherited
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.06172	Inherited
47986,52540 47986 - DEATH domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1255	Inherited
52058,52058 52058 - L domain-like 52058 - L domain-like	0.1777	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.1928	Inherited
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.2512	Inherited
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.295	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.3858	Inherited
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.4447	Inherited
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.458	Inherited
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.5971	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.0000003962	Direct
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.0000003962	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0.0004153	Direct
57184,57196,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.01124	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.2512	Inherited
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.4888	Inherited
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.6316	Inherited

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

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Mammalian Phenotype (MP): abnormal cytokine secretion

Superfamily

Family

Supra-domain (including individual superfamily)