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Phenotypic Abnormality (PA): Abnormality of the immune system
(show info)
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: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Superfamily domains annotated to this HP term (Not in SDHP)
Highlighted in gray are those with FDR_all>0.001
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this HP term (SDHP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Proteasome subunits | 0 | DIRECT |
| Animal lipoxigenases | 0 | DIRECT |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0 | DIRECT |
| Netrin-like domain (NTR/C345C module) | 0 | DIRECT |
| beta-glycanases | 0 | DIRECT |
| ets domain | 0 | DIRECT |
| Notch domain | 0 | DIRECT |
| XPF/Rad1/Mus81 nuclease | 0 | DIRECT |
| Anaphylotoxins (complement system) | 0 | DIRECT |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0 | DIRECT |
| Long-chain cytokines | 0 | DIRECT |
| C5 cytosine-specific DNA methylase, DCM | 0 | DIRECT |
| Interferon regulatory factor 3 (IRF3), transactivation domain | 0 | DIRECT |
| Fibrinogen coiled-coil and central regions | 0 | DIRECT |
| C1 set domains (antibody constant domain-like) | 0.00001626 | DIRECT |
| MHC antigen-recognition domain | 0.0002453 | DIRECT |
| DEATH domain, DD | 0.002435 | INHERITED FROM: Uveitis || Lymphadenopathy || Abnormality of B cell physiology || Abnormality of immune system physiology || Abnormal immunoglobulin level || Splenomegaly |
| SH2 domain | 0.002581 | INHERITED FROM: Abnormality of humoral immunity || Unusual infection || Unusual CNS infection || Autoimmunity || Recurrent skin infections || Abnormality of B cell physiology || Abnormal immune system morphology || Neutropenia || Abnormal cellular immune system morphology || Abnormal lymphocyte physiology |
| Complement control module/SCR domain | 0.002772 | INHERITED FROM: Recurrent Neisserial infections || Abnormality of humoral immunity || Recurrent meningococcal disease || Recurrent bacterial infections || Abnormality of immune system physiology || Abnormality of complement system |
| ABC transporter ATPase domain-like | 0.004136 | INHERITED FROM: Recurrent acute respiratory tract infection |
| TNF-like | 0.006461 | INHERITED FROM: Increased circulating IgM level || Decreased serum complement factor I || Abnormality of humoral immunity || Glomerulonephritis || Complement deficiency || Recurrent infections || Antinuclear antibody positivity || Abnormality of B cell physiology || Abnormality of immune system physiology || Nephritis || Abnormality of the lymph nodes |
| ABC transporter transmembrane region | 0.009402 | INHERITED FROM: Recurrent acute respiratory tract infection |
| Globins | 0.01472 | INHERITED FROM: Abnormality of the lymphatic system || Abnormality of the spleen || Abnormal spleen morphology || Splenomegaly |
| Ras-binding domain, RBD | 0.01472 | INHERITED FROM: Abnormality of the spleen |
| Pyrin domain, PYD | 0.0308 | INHERITED FROM: Skin rash || Abnormality of the lymphatic system || Abnormal leukocyte morphology || Recurrent aphthous stomatitis || Abnormality of the spleen || Stomatitis || Lymphadenopathy || Conjunctivitis || Keratitis || Leukocytosis || Inflammatory abnormality of the eye || Abnormal spleen morphology || Abnormal immune system morphology || Splenomegaly || Abnormal leukocyte count || Abnormal cellular immune system morphology |
| 28-residue LRR | 0.03201 | INHERITED FROM: Recurrent aphthous stomatitis || Stomatitis || Retrobulbar optic neuritis || Uveitis || Lymphadenopathy || Conjunctivitis || Leukocytosis || Optic neuritis || Unusual infection by anatomical site || Splenomegaly || Colitis |
| PX domain | 0.04738 | INHERITED FROM: Splenomegaly |
| TNF receptor-like | 0.06209 | INHERITED FROM: Abnormality of the lymphatic system || Abnormality of B cell physiology || Abnormal spleen morphology || Abnormal immunoglobulin level || Splenomegaly |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.06365 | INHERITED FROM: Recurrent respiratory infections || Otitis media |
| Tandem AAA-ATPase domain | 0.07142 | INHERITED FROM: Abnormal cellular immune system morphology |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.08626 | INHERITED FROM: Leukopenia |
| Nitrogenase iron protein-like | 0.08626 | INHERITED FROM: Lymphopenia || Abnormal leukocyte count |
| Transcription factor STAT-4 N-domain | 0.08626 | INHERITED FROM: Stomatitis || Lymphadenopathy || Leukopenia || Neutropenia || Abnormal neutrophil count || Abnormal leukocyte count |
| STAT DNA-binding domain | 0.08626 | INHERITED FROM: Stomatitis || Lymphadenopathy || Leukopenia || Neutropenia || Abnormal neutrophil count || Abnormal leukocyte count |
| STAT | 0.08626 | INHERITED FROM: Stomatitis || Lymphadenopathy || Leukopenia || Neutropenia || Abnormal neutrophil count || Abnormal leukocyte count |
| Alpha-macroglobulin receptor domain | 0.0968 | INHERITED FROM: Complement deficiency || Unusual CNS infection || Abnormality of complement system |
| Complement components | 0.0968 | INHERITED FROM: Complement deficiency || Unusual CNS infection || Abnormality of complement system |
| Fibrinogen C-terminal domain-like | 0.1009 | INHERITED FROM: Splenic rupture |
| Arylsulfatase | 0.1009 | INHERITED FROM: Recurrent upper respiratory tract infections |
| Caspase recruitment domain, CARD | 0.1528 | INHERITED FROM: Uveitis || Lymphadenopathy || Inflammatory abnormality of the eye || Abnormality of the lymph nodes |
| Eukaryotic proteases | 0.1863 | INHERITED FROM: Periodontitis || Autoimmunity || Abnormality of complement system |
| PLC-like (P variant) | 0.2531 | INHERITED FROM: Thyroiditis |
| Tetratricopeptide repeat (TPR) | 0.2551 | INHERITED FROM: Aplasia/Hypoplasia of the thymus || Hypoplasia of the thymus || Aplasia/Hypoplasia of the spleen || Asplenia |
| PHD domain | 0.2551 | INHERITED FROM: Otitis media |
| Noncollagenous (NC1) domain of collagen IV | 0.2576 | INHERITED FROM: Nephritis |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.2915 | INHERITED FROM: Glomerulonephritis || Nephritis |
| TSP-1 type 1 repeat | 0.3514 | INHERITED FROM: Recurrent Neisserial infections || Abnormality of humoral immunity || Abnormality of complement system || Recurrent gram-negative bacterial infections |
| V set domains (antibody variable domain-like) | 0.3656 | INHERITED FROM: Abnormal lymphocyte morphology |
| RecA protein-like (ATPase-domain) | 0.4324 | INHERITED FROM: Recurrent urinary tract infections |
| SH3-domain | 0.5399 | INHERITED FROM: Liver abscess |
| LDL receptor-like module | 0.675 | INHERITED FROM: Recurrent Neisserial infections || Complement deficiency || Abnormality of complement system || Recurrent gram-negative bacterial infections |
| Spermadhesin, CUB domain | 0.6907 | INHERITED FROM: Systemic lupus erythematosus || Abnormality of complement system |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Proteasome subunits | 0 | Direct |
| Animal lipoxigenases | 0 | Direct |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0 | Direct |
| Netrin-like domain (NTR/C345C module) | 0 | Direct |
| beta-glycanases | 0 | Direct |
| ets domain | 0 | Direct |
| Notch domain | 0 | Direct |
| XPF/Rad1/Mus81 nuclease | 0 | Direct |
| Anaphylotoxins (complement system) | 0 | Direct |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0 | Direct |
| Long-chain cytokines | 0 | Direct |
| C5 cytosine-specific DNA methylase, DCM | 0 | Direct |
| Interferon regulatory factor 3 (IRF3), transactivation domain | 0 | Direct |
| Fibrinogen coiled-coil and central regions | 0 | Direct |
| C1 set domains (antibody constant domain-like) | 0.00001626 | Direct |
| MHC antigen-recognition domain | 0.0002453 | Direct |
| DEATH domain, DD | 0.002435 | Inherited |
| SH2 domain | 0.002581 | Inherited |
| Complement control module/SCR domain | 0.002772 | Inherited |
| ABC transporter ATPase domain-like | 0.004136 | Inherited |
| TNF-like | 0.006461 | Inherited |
| ABC transporter transmembrane region | 0.009402 | Inherited |
| Globins | 0.01472 | Inherited |
| Ras-binding domain, RBD | 0.01472 | Inherited |
| Pyrin domain, PYD | 0.0308 | Inherited |
| 28-residue LRR | 0.03201 | Inherited |
| PX domain | 0.04738 | Inherited |
| TNF receptor-like | 0.06209 | Inherited |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.06365 | Inherited |
| Tandem AAA-ATPase domain | 0.07142 | Inherited |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.08626 | Inherited |
| Nitrogenase iron protein-like | 0.08626 | Inherited |
| Transcription factor STAT-4 N-domain | 0.08626 | Inherited |
| STAT DNA-binding domain | 0.08626 | Inherited |
| STAT | 0.08626 | Inherited |
| Alpha-macroglobulin receptor domain | 0.0968 | Inherited |
| Complement components | 0.0968 | Inherited |
| Fibrinogen C-terminal domain-like | 0.1009 | Inherited |
| Arylsulfatase | 0.1009 | Inherited |
| Caspase recruitment domain, CARD | 0.1528 | Inherited |
| Eukaryotic proteases | 0.1863 | Inherited |
| PLC-like (P variant) | 0.2531 | Inherited |
| Tetratricopeptide repeat (TPR) | 0.2551 | Inherited |
| PHD domain | 0.2551 | Inherited |
| Noncollagenous (NC1) domain of collagen IV | 0.2576 | Inherited |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.2915 | Inherited |
| TSP-1 type 1 repeat | 0.3514 | Inherited |
| V set domains (antibody variable domain-like) | 0.3656 | Inherited |
| RecA protein-like (ATPase-domain) | 0.4324 | Inherited |
| SH3-domain | 0.5399 | Inherited |
| LDL receptor-like module | 0.675 | Inherited |
| Spermadhesin, CUB domain | 0.6907 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
Supra-domains annotated to this HP term (Not in SPHO)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this HP term (Not in SPHO)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0 | DIRECT |
52980,47781
52980 - Restriction endonuclease-like
47781 - RuvA domain 2-like | 0 | DIRECT |
50729,55550
50729 - PH domain-like
55550 - SH2 domain | 0 | DIRECT |
64268,50044
64268 - PX domain
50044 - SH3-domain | 0 | DIRECT |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0 | DIRECT |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0 | DIRECT |
82895,57424
82895 - TSP-1 type 1 repeat
57424 - LDL receptor-like module | 0 | DIRECT |
46579,64593
46579 - Prefoldin
64593 - Intermediate filament protein, coiled coil region | 0 | DIRECT |
49723,48484
49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain)
48484 - Lipoxigenase | 0 | DIRECT |
49410,50242
49410 - Alpha-macroglobulin receptor domain
50242 - TIMP-like | 0 | DIRECT |
52540,90123
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0 | DIRECT |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.00009058 | DIRECT |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.0001929 | DIRECT |
90123,52540
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.005562 | INHERITED FROM: Recurrent acute respiratory tract infection |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.005646 | INHERITED FROM: Splenomegaly || Abnormal immunoglobulin level || Abnormal spleen morphology || Abnormal cellular immune system morphology || Conjunctivitis || Abnormality of humoral immunity || Abnormality of B cell physiology || Abnormality of the lymphatic system |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.0115 | INHERITED FROM: Abnormal immunoglobulin level || Abnormal leukocyte count || Abnormality of B cell physiology |
47986,52540
47986 - DEATH domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.02855 | INHERITED FROM: Splenomegaly || Recurrent aphthous stomatitis || Optic neuritis || Inflammatory abnormality of the skin || Inflammatory abnormality of the eye || Leukocytosis || Abnormal spleen morphology || Conjunctivitis || Lymphadenopathy || Abnormality of the lymph nodes || Abnormality of the spleen || Skin rash || Stomatitis || Abnormality of the lymphatic system || Retrobulbar optic neuritis || Uveitis |
49854,57535
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain | 0.05941 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
48371,56112
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.05941 | INHERITED FROM: Splenomegaly |
57535,50494
57535 - Complement control module/SCR domain
50494 - Trypsin-like serine proteases | 0.05941 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.05941 | INHERITED FROM: Recurrent respiratory infections || Otitis media |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.08052 | INHERITED FROM: Abnormal leukocyte count || Lymphadenopathy || Neutropenia || Stomatitis || Leukopenia || Abnormal neutrophil count |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.08052 | INHERITED FROM: Abnormal leukocyte count || Lymphadenopathy || Neutropenia || Stomatitis || Leukopenia || Abnormal neutrophil count |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.08052 | INHERITED FROM: Abnormal leukocyte count || Lymphadenopathy || Neutropenia || Stomatitis || Leukopenia || Abnormal neutrophil count |
53300,53300
53300 - vWA-like
53300 - vWA-like | 0.1454 | INHERITED FROM: Recurrent lower respiratory tract infections |
49854,57196
49854 - Spermadhesin, CUB domain
57196 - EGF/Laminin | 0.1454 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
47986,47986
47986 - DEATH domain
47986 - DEATH domain | 0.1454 | INHERITED FROM: Lymphadenopathy || Abnormality of the lymph nodes |
57196,49854
57196 - EGF/Laminin
49854 - Spermadhesin, CUB domain | 0.2467 | INHERITED FROM: Abnormality of complement system || Systemic lupus erythematosus || Autoimmunity |
56436,56436
56436 - C-type lectin-like
56436 - C-type lectin-like | 0.4566 | INHERITED FROM: Nephritis |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0 | Direct |
52980,47781
52980 - Restriction endonuclease-like
47781 - RuvA domain 2-like | 0 | Direct |
50729,55550
50729 - PH domain-like
55550 - SH2 domain | 0 | Direct |
64268,50044
64268 - PX domain
50044 - SH3-domain | 0 | Direct |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0 | Direct |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0 | Direct |
82895,57424
82895 - TSP-1 type 1 repeat
57424 - LDL receptor-like module | 0 | Direct |
46579,64593
46579 - Prefoldin
64593 - Intermediate filament protein, coiled coil region | 0 | Direct |
49723,48484
49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain)
48484 - Lipoxigenase | 0 | Direct |
49410,50242
49410 - Alpha-macroglobulin receptor domain
50242 - TIMP-like | 0 | Direct |
52540,90123
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0 | Direct |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.00009058 | Direct |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.0001929 | Direct |
90123,52540
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.005562 | Inherited |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.005646 | Inherited |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.0115 | Inherited |
47986,52540
47986 - DEATH domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.02855 | Inherited |
49854,57535
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain | 0.05941 | Inherited |
48371,56112
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.05941 | Inherited |
57535,50494
57535 - Complement control module/SCR domain
50494 - Trypsin-like serine proteases | 0.05941 | Inherited |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.05941 | Inherited |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.08052 | Inherited |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.08052 | Inherited |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.08052 | Inherited |
53300,53300
53300 - vWA-like
53300 - vWA-like | 0.1454 | Inherited |
49854,57196
49854 - Spermadhesin, CUB domain
57196 - EGF/Laminin | 0.1454 | Inherited |
47986,47986
47986 - DEATH domain
47986 - DEATH domain | 0.1454 | Inherited |
57196,49854
57196 - EGF/Laminin
49854 - Spermadhesin, CUB domain | 0.2467 | Inherited |
56436,56436
56436 - C-type lectin-like
56436 - C-type lectin-like | 0.4566 | Inherited |
(show details)
Supra-domains annotated to this HP term (Not in SPHO)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50729,55550,56112
50729 - PH domain-like
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
55550,56112,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
52540,90123,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
57196,57196,90193
57196 - EGF/Laminin
57196 - EGF/Laminin
90193 - Notch domain | 0 | DIRECT |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
90123,52540,90123
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0 | DIRECT |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.0004798 | DIRECT |
57586,57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.05941 | INHERITED FROM: Splenomegaly |
57196,49854,57535
57196 - EGF/Laminin
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain | 0.05941 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
49854,57535,57535
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.05941 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
57535,57535,50494
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
50494 - Trypsin-like serine proteases | 0.05941 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.08052 | INHERITED FROM: Abnormal leukocyte count || Lymphadenopathy || Neutropenia || Stomatitis || Leukopenia || Abnormal neutrophil count |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.08052 | INHERITED FROM: Abnormal leukocyte count || Lymphadenopathy || Neutropenia || Stomatitis || Leukopenia || Abnormal neutrophil count |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.08052 | INHERITED FROM: Autoimmunity |
49854,57196,49854
49854 - Spermadhesin, CUB domain
57196 - EGF/Laminin
49854 - Spermadhesin, CUB domain | 0.1454 | INHERITED FROM: Abnormality of complement system || Abnormality of humoral immunity || Systemic lupus erythematosus || Autoimmunity |
52540,52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.2343 | INHERITED FROM: Asplenia || Aplasia/Hypoplasia of the spleen || Chronic otitis media || Chronic sinusitis || Sinusitis |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50729,55550,56112
50729 - PH domain-like
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0 | Direct |
55550,56112,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0 | Direct |
52540,90123,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
57196,57196,90193
57196 - EGF/Laminin
57196 - EGF/Laminin
90193 - Notch domain | 0 | Direct |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0 | Direct |
90123,52540,90123
90123 - ABC transporter transmembrane region
52540 - P-loop containing nucleoside triphosphate hydrolases
90123 - ABC transporter transmembrane region | 0 | Direct |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.0004798 | Direct |
57586,57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.05941 | Inherited |
57196,49854,57535
57196 - EGF/Laminin
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain | 0.05941 | Inherited |
49854,57535,57535
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.05941 | Inherited |
57535,57535,50494
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
50494 - Trypsin-like serine proteases | 0.05941 | Inherited |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.08052 | Inherited |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.08052 | Inherited |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.08052 | Inherited |
49854,57196,49854
49854 - Spermadhesin, CUB domain
57196 - EGF/Laminin
49854 - Spermadhesin, CUB domain | 0.1454 | Inherited |
52540,52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.2343 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
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