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Mammalian Phenotype (MP): embryo phenotype
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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology (DO) DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology (HP) HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
- Mouse Phenotype (MP) Ontology (MP) MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
- Worm Phenotype (WP) Ontology (WP) WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
- Yeast Phenotype (YP) Ontology (YP) Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
- Fly Phenotype (FP) Ontology (FP) FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
- Fly Anatomy (FA) Ontology (FA) FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
- Zebrafish Anatomy (ZA) Ontology (ZA) ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology (XA) XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
- Arabidopsis Plant Ontology (AP) Ontology (AP) As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
- Enzyme Commission (EC) Ontology (EC) Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
- DrugBank ATC (DB) Ontology (DB) In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
- UniProtKB KeyWords (KW) Ontology (KW) Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
- UniProtKB UniPathway (UP) Ontology (UP) UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
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) |
| PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | DIRECT |
| p53 DNA-binding domain-like | 0 | DIRECT |
| DNA ligase | 0 | DIRECT |
| Nuclear receptor coactivator interlocking domain | 0 | DIRECT |
| p53 tetramerization domain | 0 | DIRECT |
| Retinoblastoma tumor suppressor domains | 0 | DIRECT |
| Homeodomain | 0.00000001152 | DIRECT |
| Histone lysine methyltransferases | 0.000008241 | DIRECT |
| T-box | 0.00001354 | DIRECT |
| SMAD MH1 domain | 0.00003876 | DIRECT |
| SMAD domain | 0.00003876 | DIRECT |
| Growth factor receptor domain | 0.00005863 | DIRECT |
| Bromodomain | 0.00006792 | DIRECT |
| HLH, helix-loop-helix DNA-binding domain | 0.0003692 | DIRECT |
| Frizzled cysteine-rich domain | 0.0004741 | DIRECT |
| HMG-box | 0.000479 | DIRECT |
| DIX domain | 0.0006298 | DIRECT |
| Extracellular domain of cell surface receptors | 0.0007216 | DIRECT |
| Protein kinases, catalytic subunit | 0.001054 | INHERITED FROM: abnormal placenta vasculature |
| Forkhead DNA-binding domain | 0.001534 | INHERITED FROM: abnormal pharyngeal pouch morphology || decreased somite size || abnormal mesoderm morphology |
| Transforming growth factor (TGF)-beta | 0.002149 | INHERITED FROM: absent vitelline blood vessels || broad limb buds || absent allantois || abnormal apical ectodermal ridge morphology || abnormal amniotic cavity morphology || embryonic-extraembryonic boundary constriction || abnormal anterior visceral endoderm cell migration || absent somites || abnormal visceral endoderm physiology |
| Paired domain | 0.002302 | INHERITED FROM: abnormal embryo morphology |
| Notch domain | 0.002403 | INHERITED FROM: abnormal placenta morphology || abnormal embryo development || abnormal developmental patterning |
| L domain | 0.002677 | INHERITED FROM: abnormal neural crest cell physiology |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.00521 | INHERITED FROM: decreased embryo size |
| Erythroid transcription factor GATA-1 | 0.007 | INHERITED FROM: abnormal visceral yolk sac morphology |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0.008842 | INHERITED FROM: abnormal embryo size || abnormal embryonic neuroepithelium morphology || decreased embryo size || abnormal neural tube morphology |
| Tetrahydrofolate dehydrogenase/cyclohydrolase | 0.008842 | INHERITED FROM: abnormal embryo size || decreased embryo size |
| C5 cytosine-specific DNA methylase, DCM | 0.008842 | INHERITED FROM: abnormal gastrulation || abnormal embryo turning || abnormal developmental patterning || failure of somite differentiation || impaired somite development || absent somites || abnormal somite development |
| Cullin repeat | 0.008842 | INHERITED FROM: abnormal gastrulation || abnormal developmental patterning || abnormal embryo size || decreased embryo size |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.0115 | INHERITED FROM: abnormal placental labyrinth vasculature morphology |
| Nuclear receptor | 0.01723 | INHERITED FROM: rudimentary Mullerian ducts || abnormal mesonephros morphology || abnormal chorion morphology |
| Pointed domain | 0.01983 | INHERITED FROM: abnormal extraembryonic tissue morphology |
| Cullin homology domain | 0.01983 | INHERITED FROM: abnormal parietal yolk sac morphology || abnormal embryo size || decreased embryo size || abnormal trophectoderm morphology |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0.01983 | INHERITED FROM: abnormal embryo size |
| FAD/NAD-linked reductases, N-terminal and central domains | 0.01983 | INHERITED FROM: abnormal embryo size |
| Nuclear receptor ligand-binding domain | 0.0253 | INHERITED FROM: rudimentary Mullerian ducts || abnormal mesonephros morphology || abnormal chorion morphology |
| SCF ubiquitin ligase complex WHB domain | 0.02635 | INHERITED FROM: abnormal gastrulation || abnormal developmental patterning |
| Integrin beta EGF-like domains | 0.03614 | INHERITED FROM: abnormal placenta morphology |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.03614 | INHERITED FROM: abnormal pluripotent precursor cell morphology |
| Formate/glycerate dehydrogenases, NAD-domain | 0.05273 | INHERITED FROM: abnormal embryonic neuroepithelium morphology |
| Linker histone H1/H5 | 0.05796 | INHERITED FROM: absent vitelline blood vessels || abnormal placenta physiology || rostral-caudal axis duplication || abnormal chorioallantoic fusion || abnormal rostral-caudal axis patterning || pale yolk sac || abnormal visceral yolk sac morphology || abnormal vitelline vasculature morphology || abnormal placenta development || failure of chorioallantoic fusion |
| Cell cycle transcription factor e2f-dp | 0.05796 | INHERITED FROM: abnormal trophoblast layer morphology |
| Ras-binding domain, RBD | 0.07201 | INHERITED FROM: abnormal placenta size || small placenta |
| Integrin beta tail domain | 0.08671 | INHERITED FROM: abnormal trophoblast layer morphology || abnormal preimplantation embryo morphology |
| Complement components | 0.08671 | INHERITED FROM: abnormal trophoblast layer morphology || abnormal placenta labyrinth morphology |
| Alpha-macroglobulin receptor domain | 0.08671 | INHERITED FROM: abnormal trophoblast layer morphology || abnormal placenta labyrinth morphology |
| DEP domain | 0.1161 | INHERITED FROM: craniorachischisis |
| Fibroblast growth factors (FGF) | 0.1227 | INHERITED FROM: abnormal cardiac neural crest cell migration |
| ZZ domain | 0.1265 | INHERITED FROM: abnormal vitelline vasculature morphology |
| SAM (sterile alpha motif) domain | 0.4537 | INHERITED FROM: small tail bud || abnormal tail bud morphology |
| PDZ domain | 0.6081 | INHERITED FROM: craniorachischisis |
| WW domain | 0.6324 | INHERITED FROM: abnormal rostral-caudal body axis extension |
| Ankyrin repeat | 0.7069 | INHERITED FROM: incomplete somite formation |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| PAS domain of steroid receptor coactivator 1A, NCo-A1 | 0 | Direct |
| p53 DNA-binding domain-like | 0 | Direct |
| DNA ligase | 0 | Direct |
| Nuclear receptor coactivator interlocking domain | 0 | Direct |
| p53 tetramerization domain | 0 | Direct |
| Retinoblastoma tumor suppressor domains | 0 | Direct |
| Homeodomain | 0.00000001152 | Direct |
| Histone lysine methyltransferases | 0.000008241 | Direct |
| T-box | 0.00001354 | Direct |
| SMAD MH1 domain | 0.00003876 | Direct |
| SMAD domain | 0.00003876 | Direct |
| Growth factor receptor domain | 0.00005863 | Direct |
| Bromodomain | 0.00006792 | Direct |
| HLH, helix-loop-helix DNA-binding domain | 0.0003692 | Direct |
| Frizzled cysteine-rich domain | 0.0004741 | Direct |
| HMG-box | 0.000479 | Direct |
| DIX domain | 0.0006298 | Direct |
| Extracellular domain of cell surface receptors | 0.0007216 | Direct |
| Protein kinases, catalytic subunit | 0.001054 | Inherited |
| Forkhead DNA-binding domain | 0.001534 | Inherited |
| Transforming growth factor (TGF)-beta | 0.002149 | Inherited |
| Paired domain | 0.002302 | Inherited |
| Notch domain | 0.002403 | Inherited |
| L domain | 0.002677 | Inherited |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.00521 | Inherited |
| Erythroid transcription factor GATA-1 | 0.007 | Inherited |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0.008842 | Inherited |
| Tetrahydrofolate dehydrogenase/cyclohydrolase | 0.008842 | Inherited |
| C5 cytosine-specific DNA methylase, DCM | 0.008842 | Inherited |
| Cullin repeat | 0.008842 | Inherited |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.0115 | Inherited |
| Nuclear receptor | 0.01723 | Inherited |
| Pointed domain | 0.01983 | Inherited |
| Cullin homology domain | 0.01983 | Inherited |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0.01983 | Inherited |
| FAD/NAD-linked reductases, N-terminal and central domains | 0.01983 | Inherited |
| Nuclear receptor ligand-binding domain | 0.0253 | Inherited |
| SCF ubiquitin ligase complex WHB domain | 0.02635 | Inherited |
| Integrin beta EGF-like domains | 0.03614 | Inherited |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.03614 | Inherited |
| Formate/glycerate dehydrogenases, NAD-domain | 0.05273 | Inherited |
| Linker histone H1/H5 | 0.05796 | Inherited |
| Cell cycle transcription factor e2f-dp | 0.05796 | Inherited |
| Ras-binding domain, RBD | 0.07201 | Inherited |
| Integrin beta tail domain | 0.08671 | Inherited |
| Complement components | 0.08671 | Inherited |
| Alpha-macroglobulin receptor domain | 0.08671 | Inherited |
| DEP domain | 0.1161 | Inherited |
| Fibroblast growth factors (FGF) | 0.1227 | Inherited |
| ZZ domain | 0.1265 | Inherited |
| SAM (sterile alpha motif) domain | 0.4537 | Inherited |
| PDZ domain | 0.6081 | Inherited |
| WW domain | 0.6324 | Inherited |
| Ankyrin repeat | 0.7069 | 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.
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Supra-domain (including individual superfamily)
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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) |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0 | DIRECT |
90193,90193
90193 - Notch domain
90193 - Notch domain | 0 | DIRECT |
57196,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | DIRECT |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | DIRECT |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.0001469 | DIRECT |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.0004061 | DIRECT |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.00229 | INHERITED FROM: abnormal neural crest cell migration || abnormal neural crest cell physiology |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00229 | INHERITED FROM: abnormal neural crest cell migration || abnormal neural crest cell physiology |
52113,52113
52113 - BRCT domain
52113 - BRCT domain | 0.00229 | INHERITED FROM: abnormal gastrulation || abnormal embryo development |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.004434 | INHERITED FROM: decreased embryo size |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.005536 | INHERITED FROM: abnormal pharyngeal arch artery morphology || rudimentary Mullerian ducts || abnormal mesonephros morphology |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.006773 | INHERITED FROM: abnormal embryonic tissue morphology || abnormal vitelline vascular remodeling || incomplete somite formation |
57196,63825
57196 - EGF/Laminin
63825 - YWTD domain | 0.007646 | INHERITED FROM: abnormal embryonic tissue morphology |
48452,81901
48452 - TPR-like
81901 - HCP-like | 0.007849 | INHERITED FROM: abnormal neural tube morphology |
74788,75632
74788 - Cullin repeat-like
75632 - Cullin homology domain | 0.007849 | INHERITED FROM: abnormal gastrulation || abnormal developmental patterning || decreased embryo size || abnormal embryo size |
53300,69179
53300 - vWA-like
69179 - Integrin domains | 0.01761 | INHERITED FROM: abnormal placenta morphology || abnormal extraembryonic tissue morphology |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0.01761 | INHERITED FROM: abnormal embryo size |
63501,50242
63501 - Frizzled cysteine-rich domain
50242 - TIMP-like | 0.02393 | INHERITED FROM: impaired somite development || abnormal rostral-caudal axis patterning || abnormal neural tube closure || abnormal neural tube morphology || abnormal somite size || spina bifida || abnormal developmental patterning || abnormal somite development || abnormal rostral-caudal body axis extension || fused somites || decreased somite size || incomplete somite formation || embryonic growth retardation || craniorachischisis || open neural tube |
75632,46785
75632 - Cullin homology domain
46785 - "Winged helix" DNA-binding domain | 0.02393 | INHERITED FROM: abnormal gastrulation || abnormal developmental patterning |
57903,47370
57903 - FYVE/PHD zinc finger
47370 - Bromodomain | 0.04822 | INHERITED FROM: abnormal developmental patterning |
52283,51735
52283 - Formate/glycerate dehydrogenase catalytic domain-like
51735 - NAD(P)-binding Rossmann-fold domains | 0.04822 | INHERITED FROM: abnormal embryonic neuroepithelium morphology |
57196,69687
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.07967 | INHERITED FROM: abnormal trophoblast layer morphology || abnormal placenta morphology || abnormal preimplantation embryo morphology |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.09788 | INHERITED FROM: failure of chorioallantoic fusion |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.1326 | INHERITED FROM: enlarged placenta || abnormal maternal decidual layer morphology || abnormal placenta metrial gland morphology |
51045,51045
51045 - WW domain
51045 - WW domain | 0.1748 | INHERITED FROM: abnormal rostral-caudal body axis extension |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.3407 | INHERITED FROM: delayed neural tube closure |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.3665 | INHERITED FROM: incomplete somite formation |
54236,47031
54236 - Ubiquitin-like
47031 - Second domain of FERM | 0.7093 | INHERITED FROM: abnormal ectoderm development || abnormal mesoderm development |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0 | Direct |
90193,90193
90193 - Notch domain
90193 - Notch domain | 0 | Direct |
57196,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | Direct |
49417,47719
49417 - p53-like transcription factors
47719 - p53 tetramerization domain | 0 | Direct |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.0001469 | Direct |
57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.0004061 | Direct |
52058,57184
52058 - L domain-like
57184 - Growth factor receptor domain | 0.00229 | Inherited |
57184,52058
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00229 | Inherited |
52113,52113
52113 - BRCT domain
52113 - BRCT domain | 0.00229 | Inherited |
49417,81296
49417 - p53-like transcription factors
81296 - E set domains | 0.004434 | Inherited |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.005536 | Inherited |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.006773 | Inherited |
57196,63825
57196 - EGF/Laminin
63825 - YWTD domain | 0.007646 | Inherited |
48452,81901
48452 - TPR-like
81901 - HCP-like | 0.007849 | Inherited |
74788,75632
74788 - Cullin repeat-like
75632 - Cullin homology domain | 0.007849 | Inherited |
53300,69179
53300 - vWA-like
69179 - Integrin domains | 0.01761 | Inherited |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0.01761 | Inherited |
63501,50242
63501 - Frizzled cysteine-rich domain
50242 - TIMP-like | 0.02393 | Inherited |
75632,46785
75632 - Cullin homology domain
46785 - "Winged helix" DNA-binding domain | 0.02393 | Inherited |
57903,47370
57903 - FYVE/PHD zinc finger
47370 - Bromodomain | 0.04822 | Inherited |
52283,51735
52283 - Formate/glycerate dehydrogenase catalytic domain-like
51735 - NAD(P)-binding Rossmann-fold domains | 0.04822 | Inherited |
57196,69687
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.07967 | Inherited |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.09788 | Inherited |
49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.1326 | Inherited |
51045,51045
51045 - WW domain
51045 - WW domain | 0.1748 | Inherited |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.3407 | Inherited |
49313,49313
49313 - Cadherin-like
49313 - Cadherin-like | 0.3665 | Inherited |
54236,47031
54236 - Ubiquitin-like
47031 - Second domain of FERM | 0.7093 | 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 |
63825,57196,57424
63825 - YWTD domain
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | DIRECT |
57196,57424,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0 | DIRECT |
57196,90193,90193
57196 - EGF/Laminin
90193 - Notch domain
90193 - Notch domain | 0 | DIRECT |
54928,54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0 | DIRECT |
63825,57196,63825
63825 - YWTD domain
57196 - EGF/Laminin
63825 - YWTD domain | 0.0005356 | DIRECT |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.002093 | INHERITED FROM: abnormal neural tube morphology |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00229 | INHERITED FROM: abnormal neural crest cell migration || abnormal neural crest cell physiology |
57196,63825,57196
57196 - EGF/Laminin
63825 - YWTD domain
57196 - EGF/Laminin | 0.007646 | INHERITED FROM: abnormal embryonic tissue morphology |
57196,57184,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.007646 | INHERITED FROM: pale yolk sac || abnormal extraembryonic tissue morphology |
74788,75632,46785
74788 - Cullin repeat-like
75632 - Cullin homology domain
46785 - "Winged helix" DNA-binding domain | 0.007849 | INHERITED FROM: abnormal gastrulation || abnormal developmental patterning || decreased embryo size || abnormal embryo size |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.01761 | INHERITED FROM: abnormal embryo size |
57667,57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.07732 | INHERITED FROM: absent floor plate |
57196,57196,69687
57196 - EGF/Laminin
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.07967 | INHERITED FROM: abnormal trophoblast layer morphology || abnormal placenta morphology || abnormal preimplantation embryo morphology |
57184,57184,57196
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.07967 | INHERITED FROM: abnormal placenta morphology |
48726,49265,49265
48726 - Immunoglobulin
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.1748 | INHERITED FROM: abnormal extraembryonic tissue physiology |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.2483 | INHERITED FROM: delayed neural tube closure |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.3095 | INHERITED FROM: incomplete somite formation |
54236,47031,50729
54236 - Ubiquitin-like
47031 - Second domain of FERM
50729 - PH domain-like | 0.7093 | INHERITED FROM: abnormal ectoderm development || abnormal mesoderm 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 |
63825,57196,57424
63825 - YWTD domain
57196 - EGF/Laminin
57424 - LDL receptor-like module | 0 | Direct |
57196,57424,57424
57196 - EGF/Laminin
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0 | Direct |
57196,90193,90193
57196 - EGF/Laminin
90193 - Notch domain
90193 - Notch domain | 0 | Direct |
54928,54928,54928
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD
54928 - RNA-binding domain, RBD | 0 | Direct |
63825,57196,63825
63825 - YWTD domain
57196 - EGF/Laminin
63825 - YWTD domain | 0.0005356 | Direct |
57184,49899,49899
57184 - Growth factor receptor domain
49899 - Concanavalin A-like lectins/glucanases
49899 - Concanavalin A-like lectins/glucanases | 0.002093 | Inherited |
52058,57184,52058
52058 - L domain-like
57184 - Growth factor receptor domain
52058 - L domain-like | 0.00229 | Inherited |
57196,63825,57196
57196 - EGF/Laminin
63825 - YWTD domain
57196 - EGF/Laminin | 0.007646 | Inherited |
57196,57184,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain | 0.007646 | Inherited |
74788,75632,46785
74788 - Cullin repeat-like
75632 - Cullin homology domain
46785 - "Winged helix" DNA-binding domain | 0.007849 | Inherited |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0.01761 | Inherited |
57667,57667,57667
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers
57667 - beta-beta-alpha zinc fingers | 0.07732 | Inherited |
57196,57196,69687
57196 - EGF/Laminin
57196 - EGF/Laminin
69687 - Integrin beta tail domain | 0.07967 | Inherited |
57184,57184,57196
57184 - Growth factor receptor domain
57184 - Growth factor receptor domain
57196 - EGF/Laminin | 0.07967 | Inherited |
48726,49265,49265
48726 - Immunoglobulin
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.1748 | Inherited |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.2483 | Inherited |
49313,49313,49313
49313 - Cadherin-like
49313 - Cadherin-like
49313 - Cadherin-like | 0.3095 | Inherited |
54236,47031,50729
54236 - Ubiquitin-like
47031 - Second domain of FERM
50729 - PH domain-like | 0.7093 | 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
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