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Worm Phenotype (WP): cell homeostasis metabolism variant
(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: WP Hierarchy (worm phenotype from Wormbase Release WS226)
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 WP term (SDWP level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Sir2 family of transcriptional regulators | 0 | DIRECT |
| Heat shock protein 90, HSP90, N-terminal domain | 0 | DIRECT |
| Nucleosome core histones | 0 | DIRECT |
| Heme-dependent catalases | 0 | DIRECT |
| Lipovitellin-phosvitin complex, superhelical domain | 0 | DIRECT |
| Hsp90 middle domain | 0 | DIRECT |
| Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | DIRECT |
| XPF/Rad1/Mus81 nuclease | 0 | DIRECT |
| Smc hinge domain | 0 | DIRECT |
| RNA-polymerase beta | 0 | DIRECT |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0 | DIRECT |
| Histone deacetylase, HDAC | 0 | DIRECT |
| Mammalian PLC | 0 | DIRECT |
| LEM domain | 0 | DIRECT |
| HSP90 C-terminal domain | 0 | DIRECT |
| Integrin domains | 0 | DIRECT |
| Arginine methyltransferase | 0 | DIRECT |
| PLC-like (P variant) | 0.00000005806 | DIRECT |
| Cyclin | 0.0004155 | DIRECT |
| Cdc48 domain 2-like | 0.0007595 | DIRECT |
| Hemocyanin middle domain | 0.0007595 | DIRECT |
| Cdc48 N-terminal domain-like | 0.0007595 | DIRECT |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.000818 | DIRECT |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.001863 | INHERITED FROM: mitochondrial metabolism variant || autophagy variant |
| RING finger domain, C3HC4 | 0.004086 | INHERITED FROM: germ cell hypersensitive ionizing radiation || germ cell ionizing radiation response variant |
| I set domains | 0.01002 | INHERITED FROM: protein degradation variant |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.01231 | INHERITED FROM: response to injury variant |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.01718 | INHERITED FROM: chromosome segregation variant || sister chromatid segregation defective early emb |
| Calpain large subunit, middle domain (domain III) | 0.01718 | INHERITED FROM: protein metabolism variant || protein degradation variant |
| Calpain large subunit, catalytic domain (domain II) | 0.01718 | INHERITED FROM: protein metabolism variant || protein degradation variant |
| Motor proteins | 0.02866 | INHERITED FROM: meiotic chromosome segregation variant || chromosome segregation variant || X chromosome nondisjunction |
| Histone lysine methyltransferases | 0.0304 | INHERITED FROM: protein modification variant || protein metabolism variant || protein methylation variant || histone methylation variant |
| Hect, E3 ligase catalytic domain | 0.03573 | INHERITED FROM: cell ionizing radiation response variant || germ cell ionizing radiation response variant |
| Pleckstrin-homology domain (PH domain) | 0.05527 | INHERITED FROM: cellular osmotic stress response variant || protein degradation variant || cell stress response variant || protein phosphorylation reduced |
| Protein kinases, catalytic subunit | 0.05646 | INHERITED FROM: protein modification variant || protein phosphorylation variant || protein phosphorylation reduced |
| Tandem AAA-ATPase domain | 0.05722 | INHERITED FROM: G tract instability || cell stress response variant |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0.0734 | INHERITED FROM: unfolded protein response variant || protein metabolism variant || cell stress response variant |
| F1F0 ATP synthase subunit C | 0.0734 | INHERITED FROM: protein metabolism variant || protein transport variant |
| EF-hand modules in multidomain proteins | 0.0734 | INHERITED FROM: cell stress response variant |
| Elongation factors | 0.09003 | INHERITED FROM: protein phosphorylation increased || proteasome core activity variant || protein phosphorylation variant |
| PHD domain | 0.1711 | INHERITED FROM: protein modification variant || protein methylation variant |
| Cold shock DNA-binding domain-like | 0.1982 | INHERITED FROM: mRNA surveillance defective || RNA metabolism variant |
| Spectrin repeat | 0.2406 | INHERITED FROM: protein metabolism variant || protein degradation variant |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.2406 | INHERITED FROM: unfolded protein response variant || protein metabolism variant |
| Transducin (alpha subunit), insertion domain | 0.2522 | INHERITED FROM: protein phosphorylation variant || protein phosphorylation reduced |
| Canonical RBD | 0.2751 | INHERITED FROM: organelle metabolism variant || nucleocytoplasmic transport defective || RNA processing variant || RNA metabolism variant || mRNA export variant |
| Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 0.3723 | INHERITED FROM: protein metabolism variant |
| LIM domain | 0.3723 | INHERITED FROM: protein degradation variant |
| Group II chaperonin (CCT, TRIC), apical domain | 0.3802 | INHERITED FROM: unfolded protein response variant || protein metabolism variant |
| Voltage-gated potassium channels | 0.42 | INHERITED FROM: protein degradation variant |
| ABC transporter ATPase domain-like | 0.4553 | INHERITED FROM: anaphase bridging |
| G proteins | 0.6206 | INHERITED FROM: protein metabolism variant || cellular osmotic stress response variant || protein phosphorylation variant |
| BTB/POZ domain | 1 | INHERITED FROM: meiotic chromosome segregation variant || aneuploidy || chromosome segregation variant || X chromosome nondisjunction |
| Skp1 dimerisation domain-like | 1 | INHERITED FROM: meiotic chromosome segregation variant || aneuploidy || X chromosome nondisjunction |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Sir2 family of transcriptional regulators | 0 | Direct |
| Heat shock protein 90, HSP90, N-terminal domain | 0 | Direct |
| Nucleosome core histones | 0 | Direct |
| Heme-dependent catalases | 0 | Direct |
| Lipovitellin-phosvitin complex, superhelical domain | 0 | Direct |
| Hsp90 middle domain | 0 | Direct |
| Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | Direct |
| XPF/Rad1/Mus81 nuclease | 0 | Direct |
| Smc hinge domain | 0 | Direct |
| RNA-polymerase beta | 0 | Direct |
| Phoshoinositide 3-kinase (PI3K) helical domain | 0 | Direct |
| Histone deacetylase, HDAC | 0 | Direct |
| Mammalian PLC | 0 | Direct |
| LEM domain | 0 | Direct |
| HSP90 C-terminal domain | 0 | Direct |
| Integrin domains | 0 | Direct |
| Arginine methyltransferase | 0 | Direct |
| PLC-like (P variant) | 0.00000005806 | Direct |
| Cyclin | 0.0004155 | Direct |
| Cdc48 domain 2-like | 0.0007595 | Direct |
| Hemocyanin middle domain | 0.0007595 | Direct |
| Cdc48 N-terminal domain-like | 0.0007595 | Direct |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.000818 | Direct |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.001863 | Inherited |
| RING finger domain, C3HC4 | 0.004086 | Inherited |
| I set domains | 0.01002 | Inherited |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.01231 | Inherited |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.01718 | Inherited |
| Calpain large subunit, middle domain (domain III) | 0.01718 | Inherited |
| Calpain large subunit, catalytic domain (domain II) | 0.01718 | Inherited |
| Motor proteins | 0.02866 | Inherited |
| Histone lysine methyltransferases | 0.0304 | Inherited |
| Hect, E3 ligase catalytic domain | 0.03573 | Inherited |
| Pleckstrin-homology domain (PH domain) | 0.05527 | Inherited |
| Protein kinases, catalytic subunit | 0.05646 | Inherited |
| Tandem AAA-ATPase domain | 0.05722 | Inherited |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0.0734 | Inherited |
| F1F0 ATP synthase subunit C | 0.0734 | Inherited |
| EF-hand modules in multidomain proteins | 0.0734 | Inherited |
| Elongation factors | 0.09003 | Inherited |
| PHD domain | 0.1711 | Inherited |
| Cold shock DNA-binding domain-like | 0.1982 | Inherited |
| Spectrin repeat | 0.2406 | Inherited |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.2406 | Inherited |
| Transducin (alpha subunit), insertion domain | 0.2522 | Inherited |
| Canonical RBD | 0.2751 | Inherited |
| Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 0.3723 | Inherited |
| LIM domain | 0.3723 | Inherited |
| Group II chaperonin (CCT, TRIC), apical domain | 0.3802 | Inherited |
| Voltage-gated potassium channels | 0.42 | Inherited |
| ABC transporter ATPase domain-like | 0.4553 | Inherited |
| G proteins | 0.6206 | Inherited |
| BTB/POZ domain | 1 | Inherited |
| Skp1 dimerisation domain-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)
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Supra-domains annotated to this WP term (SPWP 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) |
47473,51695
47473 - EF-hand
51695 - PLC-like phosphodiesterases | 0 | DIRECT |
50729,47473
50729 - PH domain-like
47473 - EF-hand | 0 | DIRECT |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0 | DIRECT |
56968,48431
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions
48431 - Lipovitellin-phosvitin complex, superhelical domain | 0 | DIRECT |
57903,51197
57903 - FYVE/PHD zinc finger
51197 - Clavaminate synthase-like | 0 | DIRECT |
54585,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
51695,49562
51695 - PLC-like phosphodiesterases
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | DIRECT |
50692,54585
50692 - ADC-like
54585 - Cdc48 domain 2-like | 0 | DIRECT |
48431,56968
48431 - Lipovitellin-phosvitin complex, superhelical domain
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | DIRECT |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.0003533 | DIRECT |
81333,81333
81333 - F1F0 ATP synthase subunit C
81333 - F1F0 ATP synthase subunit C | 0.0004294 | DIRECT |
49265,48726
49265 - Fibronectin type III
48726 - Immunoglobulin | 0.0004294 | DIRECT |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.0009351 | DIRECT |
54001,49758
54001 - Cysteine proteinases
49758 - Calpain large subunit, middle domain (domain III) | 0.01795 | INHERITED FROM: protein metabolism variant || protein degradation variant |
48726,49265
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.01843 | INHERITED FROM: protein degradation variant |
52540,50447
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins | 0.09244 | INHERITED FROM: protein phosphorylation increased || protein phosphorylation variant || proteasome core activity variant |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.1117 | INHERITED FROM: protein degradation variant |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.153 | INHERITED FROM: protein metabolism variant || unfolded protein response variant || cell stress response variant |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.153 | INHERITED FROM: protein metabolism variant || unfolded protein response variant || cell stress response variant |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.1613 | INHERITED FROM: protein phosphorylation variant || protein phosphorylation reduced |
48065,50729
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0.2447 | INHERITED FROM: protein metabolism variant |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.377 | INHERITED FROM: protein metabolism variant || protein degradation variant |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 1 | INHERITED FROM: X chromosome nondisjunction || meiotic chromosome segregation variant || aneuploidy || chromosome segregation variant |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
47473,51695
47473 - EF-hand
51695 - PLC-like phosphodiesterases | 0 | Direct |
50729,47473
50729 - PH domain-like
47473 - EF-hand | 0 | Direct |
49562,48371
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat | 0 | Direct |
56968,48431
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions
48431 - Lipovitellin-phosvitin complex, superhelical domain | 0 | Direct |
57903,51197
57903 - FYVE/PHD zinc finger
51197 - Clavaminate synthase-like | 0 | Direct |
54585,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
51695,49562
51695 - PLC-like phosphodiesterases
49562 - C2 domain (Calcium/lipid-binding domain, CaLB) | 0 | Direct |
50692,54585
50692 - ADC-like
54585 - Cdc48 domain 2-like | 0 | Direct |
48431,56968
48431 - Lipovitellin-phosvitin complex, superhelical domain
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | Direct |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.0003533 | Direct |
81333,81333
81333 - F1F0 ATP synthase subunit C
81333 - F1F0 ATP synthase subunit C | 0.0004294 | Direct |
49265,48726
49265 - Fibronectin type III
48726 - Immunoglobulin | 0.0004294 | Direct |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.0009351 | Direct |
54001,49758
54001 - Cysteine proteinases
49758 - Calpain large subunit, middle domain (domain III) | 0.01795 | Inherited |
48726,49265
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.01843 | Inherited |
52540,50447
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins | 0.09244 | Inherited |
48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.1117 | Inherited |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.153 | Inherited |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.153 | Inherited |
47895,52540
47895 - Transducin (alpha subunit), insertion domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.1613 | Inherited |
48065,50729
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like | 0.2447 | Inherited |
46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.377 | Inherited |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 1 | Inherited |
(show details)
Supra-domains annotated to this WP term (SPWP 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) |
48371,48371,48371
48371 - ARM repeat
48371 - ARM repeat
48371 - ARM repeat | 0 | DIRECT |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
50729,47473,51695
50729 - PH domain-like
47473 - EF-hand
51695 - PLC-like phosphodiesterases | 0 | DIRECT |
50692,54585,52540
50692 - ADC-like
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
54585,52540,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
56968,48431,56968
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions
48431 - Lipovitellin-phosvitin complex, superhelical domain
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | DIRECT |
52540,50447,50465
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.0003533 | DIRECT |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.0371 | INHERITED FROM: protein degradation variant |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.09244 | INHERITED FROM: protein degradation variant |
48592,54849,52029
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.153 | INHERITED FROM: protein metabolism variant || unfolded protein response variant || cell stress response variant |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.377 | INHERITED FROM: protein metabolism variant || protein degradation variant |
57716,57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.5339 | INHERITED FROM: protein degradation variant |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48371,48371,48371
48371 - ARM repeat
48371 - ARM repeat
48371 - ARM repeat | 0 | Direct |
49562,48371,56112
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48371 - ARM repeat
56112 - Protein kinase-like (PK-like) | 0 | Direct |
50729,47473,51695
50729 - PH domain-like
47473 - EF-hand
51695 - PLC-like phosphodiesterases | 0 | Direct |
50692,54585,52540
50692 - ADC-like
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
54585,52540,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
56968,48431,56968
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions
48431 - Lipovitellin-phosvitin complex, superhelical domain
56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions | 0 | Direct |
52540,50447,50465
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.0003533 | Direct |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.0371 | Inherited |
48726,48726,48726
48726 - Immunoglobulin
48726 - Immunoglobulin
48726 - Immunoglobulin | 0.09244 | Inherited |
48592,54849,52029
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.153 | Inherited |
46966,46966,46966
46966 - Spectrin repeat
46966 - Spectrin repeat
46966 - Spectrin repeat | 0.377 | Inherited |
57716,57716,57716
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain)
57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.5339 | 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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