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Mammalian Phenotype (MP): abnormal gland 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)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Hedgehog (development protein), N-terminal signaling domain | 0 | DIRECT |
| Pointed domain | 0 | DIRECT |
| PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | DIRECT |
| p53 DNA-binding domain-like | 0 | DIRECT |
| Nitric oxide (NO) synthase oxygenase domain | 0 | DIRECT |
| RUNT domain | 0 | DIRECT |
| Hedgehog C-terminal (Hog) autoprocessing domain | 0 | DIRECT |
| Nuclear receptor coactivator interlocking domain | 0 | DIRECT |
| p53 tetramerization domain | 0 | DIRECT |
| N-acetylmuramoyl-L-alanine amidase-like | 0 | DIRECT |
| E2F dimerization segment | 0 | DIRECT |
| Multidrug efflux transporter AcrB transmembrane domain | 0 | DIRECT |
| Retinoblastoma tumor suppressor domains | 0 | DIRECT |
| Cytochrome p450 reductase N-terminal domain-like | 0 | DIRECT |
| Homeodomain | 0.000000008191 | DIRECT |
| Nuclear receptor ligand-binding domain | 0.0000006649 | DIRECT |
| Nuclear receptor | 0.00000399 | DIRECT |
| Paired domain | 0.00003877 | DIRECT |
| Insulin-like | 0.00003877 | DIRECT |
| SMAD MH1 domain | 0.0001367 | DIRECT |
| SMAD domain | 0.0001367 | DIRECT |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.0002314 | DIRECT |
| SH2 domain | 0.0002357 | DIRECT |
| STAT DNA-binding domain | 0.0004696 | DIRECT |
| Transcription factor STAT-4 N-domain | 0.0004696 | DIRECT |
| L domain | 0.0004696 | DIRECT |
| STAT | 0.0004696 | DIRECT |
| CUT domain | 0.0004696 | DIRECT |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.0007579 | DIRECT |
| Growth factor receptor domain | 0.000945 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0.001281 | INHERITED FROM: pituitary gland hypoplasia || abnormal neurohypophysis morphology || abnormal neuroendocrine cell morphology || abnormal pancreatic acinar cell morphology || abnormal pancreatic acinus morphology |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.001753 | INHERITED FROM: abnormal thymus morphology || abnormal thymus medulla morphology |
| Transforming growth factor (TGF)-beta | 0.001883 | INHERITED FROM: increased ovary weight || enlarged ovary || abnormal sex gland morphology |
| PAZ domain | 0.002141 | INHERITED FROM: abnormal testis size || small testis || decreased testis weight || abnormal male reproductive gland morphology || abnormal testis weight || abnormal testis morphology |
| HMG-box | 0.003819 | INHERITED FROM: abnormal Sertoli cell morphology |
| Short-chain cytokines | 0.004361 | INHERITED FROM: abnormal female reproductive gland morphology || abnormal mammary gland development || abnormal ovarian follicle number || abnormal ovarian folliculogenesis |
| ets domain | 0.004657 | INHERITED FROM: decreased thymocyte number |
| Tudor domain | 0.004929 | INHERITED FROM: small testis || abnormal male reproductive gland morphology |
| Notch domain | 0.00498 | INHERITED FROM: abnormal sebaceous gland morphology || abnormal exocrine gland morphology || absent sebaceous gland || abnormal pancreatic acinus morphology || abnormal exocrine pancreas morphology |
| Cell cycle transcription factor e2f-dp | 0.005962 | INHERITED FROM: abnormal male reproductive gland morphology || abnormal testis morphology |
| Forkhead DNA-binding domain | 0.009131 | INHERITED FROM: abnormal pancreas development || impaired ovarian folliculogenesis || abnormal pancreatic beta cell differentiation || small pancreas || abnormal pancreatic islet morphology || abnormal pancreatic beta cell morphology |
| Extracellular domain of cell surface receptors | 0.01273 | INHERITED FROM: abnormal ovarian follicle morphology |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.0152 | INHERITED FROM: increased gland tumor incidence |
| The spindle assembly checkpoint protein mad2 | 0.01538 | INHERITED FROM: abnormal testis size || small testis || decreased testis weight || abnormal male reproductive gland morphology || abnormal testis weight || abnormal testis morphology |
| DNA gyrase/MutL, second domain | 0.01538 | INHERITED FROM: abnormal testis size || small testis || abnormal male reproductive gland morphology || abnormal testis morphology |
| DNA gyrase/MutL, N-terminal domain | 0.01538 | INHERITED FROM: abnormal testis size || small testis || abnormal male reproductive gland morphology || abnormal testis morphology |
| DNA polymerase I | 0.01691 | INHERITED FROM: increased thymus tumor incidence |
| Single strand DNA-binding domain, SSB | 0.03683 | INHERITED FROM: abnormal testis size || small testis || abnormal male reproductive gland morphology || abnormal testis morphology |
| Cysteine-rich DNA binding domain, (DM domain) | 0.03683 | INHERITED FROM: abnormal seminiferous tubule morphology |
| Transducin (alpha subunit), insertion domain | 0.04249 | INHERITED FROM: abnormal endocrine gland morphology |
| Gonadodropin/Follitropin | 0.04409 | INHERITED FROM: abnormal testis size || abnormal corpus luteum morphology || small testis || abnormal ovary size || abnormal ovary morphology || abnormal female reproductive gland morphology || abnormal seminiferous tubule morphology || abnormal ovarian follicle morphology || abnormal ovarian follicle number || small ovary |
| Long-chain cytokines | 0.07961 | INHERITED FROM: abnormal mammary gland morphology || abnormal mammary gland development || abnormal mammary gland duct morphology || abnormal apocrine gland morphology |
| Linker histone H1/H5 | 0.1007 | INHERITED FROM: small thymus || abnormal thymus size |
| DnaQ-like 3'-5' exonuclease | 0.1061 | INHERITED FROM: increased thymus tumor incidence || increased T cell derived lymphoma incidence |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.1197 | INHERITED FROM: decreased thymocyte number |
| CCCH zinc finger | 0.2368 | INHERITED FROM: increased thymus tumor incidence || increased T cell derived lymphoma incidence || abnormal thymus development |
| WW domain | 0.353 | INHERITED FROM: abnormal bile duct morphology |
| Cell cycle control phosphatase, catalytic domain | 0.3758 | INHERITED FROM: abnormal small intestine crypts of Lieberkuhn morphology || abnormal crypts of Lieberkuhn morphology |
| Phosphotyrosine-binding domain (PTB) | 0.3973 | INHERITED FROM: pancreatic islet hyperplasia || abnormal pancreatic beta cell morphology |
| EGF-type module | 0.5303 | INHERITED FROM: abnormal mammary gland duct morphology |
| LDL receptor-like module | 0.5593 | INHERITED FROM: cryptorchism |
| TNF receptor-like | 0.6242 | INHERITED FROM: abnormal thymus epithelium morphology || abnormal thymus medulla morphology || enlarged thymus |
| Cytochrome P450 | 0.6923 | INHERITED FROM: abnormal adrenal cortex morphology |
| Bcl-2 inhibitors of programmed cell death | 0.6938 | INHERITED FROM: abnormal endocrine gland morphology || abnormal ovarian follicle morphology |
| FHA domain | 0.7723 | INHERITED FROM: increased mammary adenocarcinoma incidence |
| Papain-like | 0.7723 | INHERITED FROM: abnormal thyroid gland morphology || abnormal thyroid follicle morphology |
| Intermediate filament protein, coiled coil region | 0.8071 | INHERITED FROM: abnormal holocrine gland morphology |
| DEATH domain, DD | 0.8287 | INHERITED FROM: abnormal thymus morphology || abnormal thymus medulla morphology || abnormal thymus cortex morphology |
| TNF-like | 0.8727 | INHERITED FROM: small thymus medulla || abnormal thymus epithelium morphology |
| I set domains | 0.9975 | INHERITED FROM: small endometrial glands |
| Rhodopsin-like | 1 | INHERITED FROM: abnormal pancreas weight || increased thyrotroph cell number |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Hedgehog (development protein), N-terminal signaling domain | 0 | Direct |
| Pointed domain | 0 | Direct |
| PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | Direct |
| p53 DNA-binding domain-like | 0 | Direct |
| Nitric oxide (NO) synthase oxygenase domain | 0 | Direct |
| RUNT domain | 0 | Direct |
| Hedgehog C-terminal (Hog) autoprocessing domain | 0 | Direct |
| Nuclear receptor coactivator interlocking domain | 0 | Direct |
| p53 tetramerization domain | 0 | Direct |
| N-acetylmuramoyl-L-alanine amidase-like | 0 | Direct |
| E2F dimerization segment | 0 | Direct |
| Multidrug efflux transporter AcrB transmembrane domain | 0 | Direct |
| Retinoblastoma tumor suppressor domains | 0 | Direct |
| Cytochrome p450 reductase N-terminal domain-like | 0 | Direct |
| Homeodomain | 0.000000008191 | Direct |
| Nuclear receptor ligand-binding domain | 0.0000006649 | Direct |
| Nuclear receptor | 0.00000399 | Direct |
| Paired domain | 0.00003877 | Direct |
| Insulin-like | 0.00003877 | Direct |
| SMAD MH1 domain | 0.0001367 | Direct |
| SMAD domain | 0.0001367 | Direct |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.0002314 | Direct |
| SH2 domain | 0.0002357 | Direct |
| STAT DNA-binding domain | 0.0004696 | Direct |
| Transcription factor STAT-4 N-domain | 0.0004696 | Direct |
| L domain | 0.0004696 | Direct |
| STAT | 0.0004696 | Direct |
| CUT domain | 0.0004696 | Direct |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.0007579 | Direct |
| Growth factor receptor domain | 0.000945 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0.001281 | Inherited |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.001753 | Inherited |
| Transforming growth factor (TGF)-beta | 0.001883 | Inherited |
| PAZ domain | 0.002141 | Inherited |
| HMG-box | 0.003819 | Inherited |
| Short-chain cytokines | 0.004361 | Inherited |
| ets domain | 0.004657 | Inherited |
| Tudor domain | 0.004929 | Inherited |
| Notch domain | 0.00498 | Inherited |
| Cell cycle transcription factor e2f-dp | 0.005962 | Inherited |
| Forkhead DNA-binding domain | 0.009131 | Inherited |
| Extracellular domain of cell surface receptors | 0.01273 | Inherited |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.0152 | Inherited |
| The spindle assembly checkpoint protein mad2 | 0.01538 | Inherited |
| DNA gyrase/MutL, second domain | 0.01538 | Inherited |
| DNA gyrase/MutL, N-terminal domain | 0.01538 | Inherited |
| DNA polymerase I | 0.01691 | Inherited |
| Single strand DNA-binding domain, SSB | 0.03683 | Inherited |
| Cysteine-rich DNA binding domain, (DM domain) | 0.03683 | Inherited |
| Transducin (alpha subunit), insertion domain | 0.04249 | Inherited |
| Gonadodropin/Follitropin | 0.04409 | Inherited |
| Long-chain cytokines | 0.07961 | Inherited |
| Linker histone H1/H5 | 0.1007 | Inherited |
| DnaQ-like 3'-5' exonuclease | 0.1061 | Inherited |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.1197 | Inherited |
| CCCH zinc finger | 0.2368 | Inherited |
| WW domain | 0.353 | Inherited |
| Cell cycle control phosphatase, catalytic domain | 0.3758 | Inherited |
| Phosphotyrosine-binding domain (PTB) | 0.3973 | Inherited |
| EGF-type module | 0.5303 | Inherited |
| LDL receptor-like module | 0.5593 | Inherited |
| TNF receptor-like | 0.6242 | Inherited |
| Cytochrome P450 | 0.6923 | Inherited |
| Bcl-2 inhibitors of programmed cell death | 0.6938 | Inherited |
| FHA domain | 0.7723 | Inherited |
| Papain-like | 0.7723 | Inherited |
| Intermediate filament protein, coiled coil region | 0.8071 | Inherited |
| DEATH domain, DD | 0.8287 | Inherited |
| TNF-like | 0.8727 | Inherited |
| I set domains | 0.9975 | Inherited |
| Rhodopsin-like | 1 | 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)
(show details)
Supra-domains annotated to this MP term (SPMP level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
54236,57889
54236 - Ubiquitin-like
57889 - Cysteine-rich domain | 0 | DIRECT |
55166,51294
55166 - Hedgehog/DD-peptidase
51294 - Hedgehog/intein (Hint) domain | 0 | DIRECT |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | DIRECT |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | DIRECT |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.0000649 | DIRECT |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0001647 | DIRECT |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.0003546 | DIRECT |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.0003546 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0003546 | DIRECT |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003546 | DIRECT |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.0003546 | DIRECT |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.0003546 | DIRECT |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00165 | INHERITED FROM: abnormal endocrine gland morphology || small thymus || abnormal thymus morphology || increased mammary gland tumor incidence || increased mammary adenocarcinoma incidence |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.002 | INHERITED FROM: abnormal mammary gland morphology |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0.004067 | INHERITED FROM: small testis || abnormal testis size |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.01077 | INHERITED FROM: small thymus || abnormal thymus cortex morphology |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0.01304 | INHERITED FROM: absent sebaceous gland || abnormal exocrine gland morphology || abnormal sebaceous gland morphology || abnormal holocrine gland morphology |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.02293 | INHERITED FROM: abnormal endocrine gland morphology |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.02455 | INHERITED FROM: abnormal apocrine gland morphology || abnormal mammary gland morphology |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.02455 | INHERITED FROM: abnormal endocrine gland morphology |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.02679 | INHERITED FROM: small thymus || thymus hypoplasia |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.03086 | INHERITED FROM: abnormal endocrine gland morphology || abnormal thymus epithelium morphology || abnormal thymus medulla morphology |
50249,50249
50249 - Nucleic acid-binding proteins
50249 - Nucleic acid-binding proteins | 0.03836 | INHERITED FROM: small testis || abnormal testis size |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.07197 | INHERITED FROM: absent adrenal gland || decreased DN2 thymocyte number |
90229,90229
90229 - CCCH zinc finger
90229 - CCCH zinc finger | 0.07479 | INHERITED FROM: small thymus || abnormal thymus size |
57184,57610
57184 - Growth factor receptor domain
57610 - Thyroglobulin type-1 domain | 0.07479 | INHERITED FROM: abnormal endocrine pancreas morphology || abnormal pancreatic islet morphology || abnormal pancreatic beta cell morphology || abnormal pancreas morphology |
50729,50729
50729 - PH domain-like
50729 - PH domain-like | 0.2328 | INHERITED FROM: abnormal pancreatic beta cell mass || pancreatic islet hyperplasia || enlarged pancreatic islets |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.2385 | INHERITED FROM: absent sebaceous gland || abnormal mammary gland duct morphology |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.5445 | INHERITED FROM: abnormal pituitary diverticulum morphology || abnormal Rathke's pouch development || abnormal pituitary gland development |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.8191 | INHERITED FROM: abnormal placenta metrial gland morphology || abnormal pancreatic beta cell mass |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.9833 | INHERITED FROM: small endometrial glands |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
54236,57889
54236 - Ubiquitin-like
57889 - Cysteine-rich domain | 0 | Direct |
55166,51294
55166 - Hedgehog/DD-peptidase
51294 - Hedgehog/intein (Hint) domain | 0 | Direct |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | Direct |
47576,48065
47576 - Calponin-homology domain, CH-domain
48065 - DBL homology domain (DH-domain) | 0 | Direct |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.0000649 | Direct |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.0001647 | Direct |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.0003546 | Direct |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.0003546 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.0003546 | Direct |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003546 | Direct |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.0003546 | Direct |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.0003546 | Direct |
50729,56112
50729 - PH domain-like
56112 - Protein kinase-like (PK-like) | 0.00165 | Inherited |
47459,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain) | 0.002 | Inherited |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0.004067 | Inherited |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.01077 | Inherited |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0.01304 | Inherited |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.02293 | Inherited |
55785,55785
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.02455 | Inherited |
55550,50044
55550 - SH2 domain
50044 - SH3-domain | 0.02455 | Inherited |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.02679 | Inherited |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.03086 | Inherited |
50249,50249
50249 - Nucleic acid-binding proteins
50249 - Nucleic acid-binding proteins | 0.03836 | Inherited |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.07197 | Inherited |
90229,90229
90229 - CCCH zinc finger
90229 - CCCH zinc finger | 0.07479 | Inherited |
57184,57610
57184 - Growth factor receptor domain
57610 - Thyroglobulin type-1 domain | 0.07479 | Inherited |
50729,50729
50729 - PH domain-like
50729 - PH domain-like | 0.2328 | Inherited |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.2385 | Inherited |
57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.5445 | Inherited |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.8191 | Inherited |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.9833 | Inherited |
(show details)
Supra-domains annotated to this MP term (SPMP level: Moderately Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | DIRECT |
54928,54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0 | DIRECT |
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 | 0.0003546 | DIRECT |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.0003546 | DIRECT |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003546 | DIRECT |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.003265 | INHERITED FROM: absent sebaceous gland || abnormal pancreas development |
47459,55785,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.01234 | INHERITED FROM: abnormal apocrine gland morphology || abnormal mammary gland morphology |
57184,57196,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.01411 | INHERITED FROM: absent sebaceous gland |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.04977 | INHERITED FROM: small thymus || thymus hypoplasia |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.07116 | INHERITED FROM: absent sebaceous gland || abnormal pancreas development |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57184,52058,57184
57184 - Growth factor receptor domain
52058 - L domain-like
57184 - Growth factor receptor domain | 0 | Direct |
54928,54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0 | Direct |
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 | 0.0003546 | Direct |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.0003546 | Direct |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.0003546 | Direct |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.003265 | Inherited |
47459,55785,55785
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)
55785 - PYP-like sensor domain (PAS domain) | 0.01234 | Inherited |
57184,57196,57196
57184 - Growth factor receptor domain
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.01411 | Inherited |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.04977 | Inherited |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.07116 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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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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