|
|
Mammalian Phenotype (MP): abnormal T cell morphology
(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: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Superfamily domains annotated to this MP term (Not in SDMP)
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 MP term (SDMP level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Proteasome subunits | 0 | DIRECT |
| STAT DNA-binding domain | 0 | DIRECT |
| RUNT domain | 0 | DIRECT |
| Transcription factor STAT-4 N-domain | 0 | DIRECT |
| STAT | 0 | DIRECT |
| Interleukin 17F, IL-17F | 0 | DIRECT |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.0000008244 | DIRECT |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.000005742 | DIRECT |
| MHC antigen-recognition domain | 0.0000269 | DIRECT |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.00002984 | DIRECT |
| E2F dimerization segment | 0.001083 | INHERITED FROM: decreased double-positive T cell number || abnormal T cell number || abnormal alpha-beta T cell morphology || abnormal T cell differentiation |
| Bcl-2 inhibitors of programmed cell death | 0.001353 | INHERITED FROM: abnormal T cell number || abnormal T cell differentiation |
| Interferon regulatory factor | 0.001353 | INHERITED FROM: abnormal T cell number || decreased T cell number |
| Integrin domains | 0.002165 | INHERITED FROM: decreased CD4-positive, alpha beta T cell number || decreased T cell number |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0.002783 | INHERITED FROM: abnormal CD8-positive, alpha beta T cell morphology || abnormal effector T cell morphology || abnormal CD8-positive, alpha-beta T cell number || abnormal CD4-positive, alpha beta T cell morphology || abnormal CD4-positive, alpha beta T cell number || abnormal alpha-beta T cell number |
| Nuclear receptor coactivator interlocking domain | 0.005407 | INHERITED FROM: increased T cell number |
| Cell cycle transcription factor e2f-dp | 0.009834 | INHERITED FROM: decreased double-positive T cell number || abnormal T cell differentiation |
| C1 set domains (antibody constant domain-like) | 0.03708 | INHERITED FROM: absent CD8-positive, alpha-beta T cells |
| SH2 domain | 0.3124 | INHERITED FROM: decreased single-positive T cell number || decreased thymocyte number |
| SH3-domain | 0.3461 | INHERITED FROM: abnormal CD8-positive, alpha-beta T cell differentiation || decreased single-positive T cell number |
| V set domains (antibody variable domain-like) | 0.4264 | INHERITED FROM: abnormal T-helper 17 cell morphology || abnormal T-helper 17 cell number |
| TNF receptor-like | 0.6031 | INHERITED FROM: increased CD4-positive, alpha beta T cell number || abnormal negative T cell selection |
| Pointed domain | 0.6777 | INHERITED FROM: decreased thymocyte number |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.7248 | INHERITED FROM: decreased thymocyte number || abnormal positive T cell selection |
| ets domain | 0.7853 | INHERITED FROM: decreased thymocyte number |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(show help)
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 MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0 | DIRECT |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0 | DIRECT |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0 | DIRECT |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | DIRECT |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0000005523 | DIRECT |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.000001819 | DIRECT |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00002657 | DIRECT |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.002356 | INHERITED FROM: abnormal alpha-beta T cell morphology || abnormal T cell differentiation || decreased double-positive T cell number |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0.002356 | INHERITED FROM: abnormal alpha-beta T cell morphology || abnormal effector T cell morphology || abnormal CD8-positive, alpha beta T cell morphology || abnormal CD4-positive, alpha beta T cell number || abnormal CD8-positive, alpha-beta T cell number || abnormal CD4-positive, alpha beta T cell morphology || abnormal alpha-beta T cell number |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.002828 | INHERITED FROM: decreased T cell number |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0.002828 | INHERITED FROM: decreased T cell number |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.008078 | INHERITED FROM: decreased DN2 thymocyte number |
48371,56112
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.008447 | INHERITED FROM: abnormal CD8-positive, alpha beta T cell morphology || abnormal CD4-positive, alpha beta T cell number || abnormal CD8-positive, alpha-beta T cell number || abnormal CD4-positive, alpha beta T cell morphology |
53300,69318
53300 - vWA-like
69318 - Integrin alpha N-terminal domain | 0.02931 | INHERITED FROM: increased CD8-positive, alpha-beta T cell number || increased alpha-beta T cell number || decreased CD4-positive, alpha beta T cell number |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.09714 | INHERITED FROM: abnormal mature gamma-delta T cell morphology || decreased single-positive T cell number |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.2473 | INHERITED FROM: abnormal alpha-beta T cell morphology || abnormal effector T cell morphology || decreased double-negative T cell number || decreased single-positive T cell number || abnormal double-negative T cell morphology || abnormal CD4-positive, alpha beta T cell number |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.2791 | INHERITED FROM: abnormal mature gamma-delta T cell morphology |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.5836 | INHERITED FROM: abnormal alpha-beta T cell morphology || abnormal effector T cell morphology || abnormal CD8-positive, alpha beta T cell morphology || abnormal CD4-positive, alpha beta T cell number |
47986,47986
47986 - DEATH domain
47986 - DEATH domain | 0.6751 | INHERITED FROM: abnormal CD4-positive, alpha beta T cell number |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0 | Direct |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0 | Direct |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0 | Direct |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | Direct |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0000005523 | Direct |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.000001819 | Direct |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00002657 | Direct |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.002356 | Inherited |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0.002356 | Inherited |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.002828 | Inherited |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0.002828 | Inherited |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.008078 | Inherited |
48371,56112
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.008447 | Inherited |
53300,69318
53300 - vWA-like
69318 - Integrin alpha N-terminal domain | 0.02931 | Inherited |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.09714 | Inherited |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.2473 | Inherited |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.2791 | Inherited |
55550,55550
55550 - SH2 domain
55550 - SH2 domain | 0.5836 | Inherited |
47986,47986
47986 - DEATH domain
47986 - DEATH domain | 0.6751 | Inherited |
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0 | DIRECT |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0 | DIRECT |
55550,56112,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
50729,55550,56112
50729 - PH domain-like
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
50044,55550,50044
50044 - SH3-domain
55550 - SH2 domain
50044 - SH3-domain | 0 | DIRECT |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0 | DIRECT |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0002329 | DIRECT |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.002356 | INHERITED FROM: abnormal alpha-beta T cell morphology || abnormal effector T cell morphology || abnormal CD8-positive, alpha beta T cell morphology || abnormal CD4-positive, alpha beta T cell number || abnormal CD8-positive, alpha-beta T cell number || abnormal CD4-positive, alpha beta T cell morphology || abnormal alpha-beta T cell number |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0.002828 | INHERITED FROM: decreased T cell number |
53300,69318,69179
53300 - vWA-like
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.02931 | INHERITED FROM: increased CD8-positive, alpha-beta T cell number || increased alpha-beta T cell number || decreased CD4-positive, alpha beta T cell number |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.3007 | INHERITED FROM: abnormal mature gamma-delta T cell morphology |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0 | Direct |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0 | Direct |
55550,56112,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like)
56112 - Protein kinase-like (PK-like) | 0 | Direct |
50729,55550,56112
50729 - PH domain-like
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0 | Direct |
50044,55550,50044
50044 - SH3-domain
55550 - SH2 domain
50044 - SH3-domain | 0 | Direct |
47576,48065,50729
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0 | Direct |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0002329 | Direct |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.002356 | Inherited |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0.002828 | Inherited |
53300,69318,69179
53300 - vWA-like
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0.02931 | Inherited |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.3007 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
|
Plot tree as:
| |
Download Newick format tree:
|
(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.
|
