|
Fly Phenotype (FP): increased mortality
(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: FP Hierarchy (fly phenotype from FlyBase controlled vocabulary with sub-ontology "phenotypic class")
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 FP term (SDFP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
Single strand DNA-binding domain, SSB | 0 | DIRECT |
Hsp90 middle domain | 0 | DIRECT |
beta-CASP RNA-metabolising hydrolases | 0 | DIRECT |
Fibroblast growth factors (FGF) | 0 | DIRECT |
Cu,Zn superoxide dismutase-like | 0 | DIRECT |
a tRNA synthase domain | 0 | DIRECT |
Anticodon-binding domain of Class II aaRS | 0 | DIRECT |
Extracellular domain of cell surface receptors | 0 | DIRECT |
Heat shock protein 90, HSP90, N-terminal domain | 0 | DIRECT |
Ribonuclease PH domain 2-like | 0 | DIRECT |
IF2B-like | 0 | DIRECT |
Clathrin adaptor core protein | 0 | DIRECT |
Smc hinge domain | 0 | DIRECT |
Laminin-type module | 0 | DIRECT |
Class I glutamine amidotransferases (GAT) | 0 | DIRECT |
Meta-cation ATPase, catalytic domain P | 0 | DIRECT |
Diap1 N-terninal region-like | 0 | DIRECT |
POU-specific domain | 0 | DIRECT |
MBT repeat | 0 | DIRECT |
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 0 | DIRECT |
Dachshund-homology domain | 0 | DIRECT |
Nop domain | 0 | DIRECT |
Transcriptional factor domain | 0 | DIRECT |
C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
FHA domain | 0 | DIRECT |
N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
Rel/Dorsal transcription factors, DNA-binding domain | 0 | DIRECT |
Chromo barrel domain | 0 | DIRECT |
Acyl-carrier protein (ACP) | 0 | DIRECT |
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | DIRECT |
Sec1/munc18-like (SM) proteins | 0 | DIRECT |
PAPS sulfotransferase | 0 | DIRECT |
Ubiquitin activating enzymes (UBA) | 0 | DIRECT |
NHL repeat | 0 | DIRECT |
Dimeric isocitrate & isopropylmalate dehydrogenases | 0 | DIRECT |
Isoprenyl diphosphate synthases | 0 | DIRECT |
DEK C-terminal domain | 0 | DIRECT |
RUNT domain | 0 | DIRECT |
Ribonuclease PH domain 1-like | 0 | DIRECT |
Formin homology 2 domain (FH2 domain) | 0 | DIRECT |
Succinyl-CoA synthetase domains | 0 | DIRECT |
Integrin domains | 0 | DIRECT |
Eps15 homology domain (EH domain) | 0 | DIRECT |
Subtilases | 0 | DIRECT |
B-box zinc-binding domain | 0 | DIRECT |
Group II chaperonin (CCT, TRIC), intermediate domain | 0 | DIRECT |
Inositol polyphosphate kinase (IPK) | 0 | DIRECT |
ARID domain | 0 | DIRECT |
Succinyl-CoA synthetase, beta-chain, N-terminal domain | 0 | DIRECT |
Cell cycle transcription factor e2f-dp | 0 | DIRECT |
SMAD domain | 0 | DIRECT |
SMAD MH1 domain | 0 | DIRECT |
Paired domain | 0 | DIRECT |
Multidrug efflux transporter AcrB transmembrane domain | 0 | DIRECT |
RNase III catalytic domain-like | 0 | DIRECT |
Translational machinery components | 0 | DIRECT |
MAM domain | 0 | DIRECT |
Histone lysine methyltransferases | 0 | DIRECT |
HR1 repeat | 0 | DIRECT |
Tandem AAA-ATPase domain | 0.000135 | DIRECT |
Leucine zipper domain | 0.001032 | INHERITED FROM: lethal - all die before end of larval stage || lethal - all die before end of pupal stage || lethal - all die before end of first instar larval stage |
Canonical RBD | 0.002976 | INHERITED FROM: lethal |
Protein kinases, catalytic subunit | 0.01401 | INHERITED FROM: lethal - all die before end of larval stage || lethal - all die before end of P-stage |
Homeodomain | 0.03084 | INHERITED FROM: some die during embryonic stage || lethal - all die before end of larval stage || some die during pharate adult stage || lethal - all die before end of first instar larval stage || increased mortality during development || lethal - all die before end of embryonic stage |
Nuclear receptor | 0.03751 | INHERITED FROM: lethal || increased mortality during development |
Nuclear receptor ligand-binding domain | 0.06025 | INHERITED FROM: lethal |
Spectrin repeat | 0.1021 | INHERITED FROM: lethal - all die before end of larval stage || lethal - all die before end of pupal stage || lethal - all die before end of prepupal stage |
Motor proteins | 0.1275 | INHERITED FROM: lethal - all die before end of larval stage || lethal - all die before end of first instar larval stage || lethal - all die before end of embryonic stage |
EGF-type module | 0.1673 | INHERITED FROM: lethal - all die before end of larval stage || some die during pupal stage || lethal - all die before end of prepupal stage |
Erythroid transcription factor GATA-1 | 0.2812 | INHERITED FROM: lethal - all die before end of second instar larval stage || lethal - all die before end of first instar larval stage |
Zf-UBP | 0.6442 | INHERITED FROM: some die during pupal stage |
SCOP term | FDR (all) | Annotation (direct or inherited) |
Single strand DNA-binding domain, SSB | 0 | Direct |
Hsp90 middle domain | 0 | Direct |
beta-CASP RNA-metabolising hydrolases | 0 | Direct |
Fibroblast growth factors (FGF) | 0 | Direct |
Cu,Zn superoxide dismutase-like | 0 | Direct |
a tRNA synthase domain | 0 | Direct |
Anticodon-binding domain of Class II aaRS | 0 | Direct |
Extracellular domain of cell surface receptors | 0 | Direct |
Heat shock protein 90, HSP90, N-terminal domain | 0 | Direct |
Ribonuclease PH domain 2-like | 0 | Direct |
IF2B-like | 0 | Direct |
Clathrin adaptor core protein | 0 | Direct |
Smc hinge domain | 0 | Direct |
Laminin-type module | 0 | Direct |
Class I glutamine amidotransferases (GAT) | 0 | Direct |
Meta-cation ATPase, catalytic domain P | 0 | Direct |
Diap1 N-terninal region-like | 0 | Direct |
POU-specific domain | 0 | Direct |
MBT repeat | 0 | Direct |
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 0 | Direct |
Dachshund-homology domain | 0 | Direct |
Nop domain | 0 | Direct |
Transcriptional factor domain | 0 | Direct |
C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
FHA domain | 0 | Direct |
N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
Rel/Dorsal transcription factors, DNA-binding domain | 0 | Direct |
Chromo barrel domain | 0 | Direct |
Acyl-carrier protein (ACP) | 0 | Direct |
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | Direct |
Sec1/munc18-like (SM) proteins | 0 | Direct |
PAPS sulfotransferase | 0 | Direct |
Ubiquitin activating enzymes (UBA) | 0 | Direct |
NHL repeat | 0 | Direct |
Dimeric isocitrate & isopropylmalate dehydrogenases | 0 | Direct |
Isoprenyl diphosphate synthases | 0 | Direct |
DEK C-terminal domain | 0 | Direct |
RUNT domain | 0 | Direct |
Ribonuclease PH domain 1-like | 0 | Direct |
Formin homology 2 domain (FH2 domain) | 0 | Direct |
Succinyl-CoA synthetase domains | 0 | Direct |
Integrin domains | 0 | Direct |
Eps15 homology domain (EH domain) | 0 | Direct |
Subtilases | 0 | Direct |
B-box zinc-binding domain | 0 | Direct |
Group II chaperonin (CCT, TRIC), intermediate domain | 0 | Direct |
Inositol polyphosphate kinase (IPK) | 0 | Direct |
ARID domain | 0 | Direct |
Succinyl-CoA synthetase, beta-chain, N-terminal domain | 0 | Direct |
Cell cycle transcription factor e2f-dp | 0 | Direct |
SMAD domain | 0 | Direct |
SMAD MH1 domain | 0 | Direct |
Paired domain | 0 | Direct |
Multidrug efflux transporter AcrB transmembrane domain | 0 | Direct |
RNase III catalytic domain-like | 0 | Direct |
Translational machinery components | 0 | Direct |
MAM domain | 0 | Direct |
Histone lysine methyltransferases | 0 | Direct |
HR1 repeat | 0 | Direct |
Tandem AAA-ATPase domain | 0.000135 | Direct |
Leucine zipper domain | 0.001032 | Inherited |
Canonical RBD | 0.002976 | Inherited |
Protein kinases, catalytic subunit | 0.01401 | Inherited |
Homeodomain | 0.03084 | Inherited |
Nuclear receptor | 0.03751 | Inherited |
Nuclear receptor ligand-binding domain | 0.06025 | Inherited |
Spectrin repeat | 0.1021 | Inherited |
Motor proteins | 0.1275 | Inherited |
EGF-type module | 0.1673 | Inherited |
Erythroid transcription factor GATA-1 | 0.2812 | Inherited |
Zf-UBP | 0.6442 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
(show details)
Supra-domains annotated to this FP term (SPFP level: Least 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) |
48425,50729 48425 - Sec7 domain 50729 - PH domain-like | 0 | DIRECT |
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains | 0 | DIRECT |
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain | 0 | DIRECT |
57850,57850 57850 - RING/U-box 57850 - RING/U-box | 0 | DIRECT |
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat | 0 | DIRECT |
50615,52540 50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
54211,55666 54211 - Ribosomal protein S5 domain 2-like 55666 - Ribonuclease PH domain 2-like | 0 | DIRECT |
63748,63748 63748 - Tudor/PWWP/MBT 63748 - Tudor/PWWP/MBT | 0 | DIRECT |
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region | 0 | DIRECT |
50044,55550 50044 - SH3-domain 55550 - SH2 domain | 0 | DIRECT |
55681,52954 55681 - Class II aaRS and biotin synthetases 52954 - Class II aaRS ABD-related | 0 | DIRECT |
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
52113,52113 52113 - BRCT domain 52113 - BRCT domain | 0 | DIRECT |
49417,81296 49417 - p53-like transcription factors 81296 - E set domains | 0 | DIRECT |
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | DIRECT |
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like | 0 | DIRECT |
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain | 0 | DIRECT |
57196,49854 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain | 0 | DIRECT |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48425,50729 48425 - Sec7 domain 50729 - PH domain-like | 0 | Direct |
56059,52210 56059 - Glutathione synthetase ATP-binding domain-like 52210 - Succinyl-CoA synthetase domains | 0 | Direct |
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain | 0 | Direct |
57850,57850 57850 - RING/U-box 57850 - RING/U-box | 0 | Direct |
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat | 0 | Direct |
50615,52540 50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase 52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
54211,55666 54211 - Ribosomal protein S5 domain 2-like 55666 - Ribonuclease PH domain 2-like | 0 | Direct |
63748,63748 63748 - Tudor/PWWP/MBT 63748 - Tudor/PWWP/MBT | 0 | Direct |
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) | 0 | Direct |
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region | 0 | Direct |
50044,55550 50044 - SH3-domain 55550 - SH2 domain | 0 | Direct |
55681,52954 55681 - Class II aaRS and biotin synthetases 52954 - Class II aaRS ABD-related | 0 | Direct |
52540,47917 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
52113,52113 52113 - BRCT domain 52113 - BRCT domain | 0 | Direct |
49417,81296 49417 - p53-like transcription factors 81296 - E set domains | 0 | Direct |
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 0 | Direct |
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like | 0 | Direct |
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain | 0 | Direct |
57196,49854 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain | 0 | Direct |
(show details)
Supra-domains annotated to this FP term (SPFP level: Least 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) |
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
48452,48452,48452 48452 - TPR-like 48452 - TPR-like 48452 - TPR-like | 0 | DIRECT |
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box | 0 | DIRECT |
50615,52540,47917 50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0 | DIRECT |
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat | 0 | DIRECT |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.3506 | INHERITED FROM: lethal - all die before end of embryonic stage || lethal - all die before end of first instar larval stage || some die during embryonic stage |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
48452,48452,48452 48452 - TPR-like 48452 - TPR-like 48452 - TPR-like | 0 | Direct |
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box | 0 | Direct |
50615,52540,47917 50615 - N-terminal domain of alpha and beta subunits of F1 ATP synthase 52540 - P-loop containing nucleoside triphosphate hydrolases 47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases | 0 | Direct |
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat | 0 | Direct |
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.3506 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
 |
Plot tree as:
| |
Download Newick format tree:
|
(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domains and supradomains
for all genomes in SUPERFAMILY. The RAxML
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
|