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Mammalian Phenotype (MP): abnormal retina morphology
(show info)
Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology (DO) DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology (HP) HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
- Mouse Phenotype (MP) Ontology (MP) MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
- Worm Phenotype (WP) Ontology (WP) WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
- Yeast Phenotype (YP) Ontology (YP) Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
- Fly Phenotype (FP) Ontology (FP) FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
- Fly Anatomy (FA) Ontology (FA) FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
- Zebrafish Anatomy (ZA) Ontology (ZA) ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology (XA) XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
- Arabidopsis Plant Ontology (AP) Ontology (AP) As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
- Enzyme Commission (EC) Ontology (EC) Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
- DrugBank ATC (DB) Ontology (DB) In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
- UniProtKB KeyWords (KW) Ontology (KW) Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
- UniProtKB UniPathway (UP) Ontology (UP) UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Root: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Superfamily domains annotated to this MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this MP term (Not in SDMP)
Highlighted in gray are those with FDR_all>0.001
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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Plot tree as:
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Download Newick format tree:
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(show help)
Trees by TreeVector
A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
on their own, and allows the trees to be displayed instantly.
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
90193,90193
90193 - Notch domain
90193 - Notch domain | 0 | DIRECT |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.000009739 | DIRECT |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0.00006434 | DIRECT |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.0001245 | DIRECT |
81296,81296
81296 - E set domains
81296 - E set domains | 0.0002761 | DIRECT |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0.0003718 | DIRECT |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0004145 | DIRECT |
55781,55781
55781 - GAF domain-like
55781 - GAF domain-like | 0.003132 | INHERITED FROM: retinal photoreceptor degeneration || abnormal retinal neuronal layer morphology || abnormal retinal photoreceptor morphology || abnormal retinal photoreceptor layer morphology || abnormal retinal layer morphology || decreased retinal photoreceptor cell number |
55781,109604
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.003132 | INHERITED FROM: retinal photoreceptor degeneration || abnormal retinal neuronal layer morphology || abnormal retinal photoreceptor morphology || abnormal retinal photoreceptor layer morphology || abnormal retinal layer morphology || decreased retinal photoreceptor cell number |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.00586 | INHERITED FROM: abnormal retinal neuronal layer morphology || abnormal retinal ganglion layer morphology || abnormal retinal ganglion cell morphology || decreased retinal ganglion cell number || abnormal retinal bipolar cell morphology |
101288,50156
101288 - L27 domain
50156 - PDZ domain-like | 0.00586 | INHERITED FROM: abnormal retinal neuronal layer morphology |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.02225 | INHERITED FROM: retina hypoplasia |
47090,55486
47090 - PGBD-like
55486 - Metalloproteases ("zincins"), catalytic domain | 0.1048 | INHERITED FROM: retinal neovascularization || abnormal induced retinal neovascularization |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.1338 | INHERITED FROM: abnormal retinal ganglion cell morphology |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
90193,90193
90193 - Notch domain
90193 - Notch domain | 0 | Direct |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.000009739 | Direct |
101912,103575
101912 - Sema domain
103575 - Plexin repeat | 0.00006434 | Direct |
57716,48508
57716 - Glucocorticoid receptor-like (DNA-binding domain)
48508 - Nuclear receptor ligand-binding domain | 0.0001245 | Direct |
81296,81296
81296 - E set domains
81296 - E set domains | 0.0002761 | Direct |
57196,90193
57196 - EGF/Laminin
90193 - Notch domain | 0.0003718 | Direct |
57196,57184
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.0004145 | Direct |
55781,55781
55781 - GAF domain-like
55781 - GAF domain-like | 0.003132 | Inherited |
55781,109604
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.003132 | Inherited |
46785,144074
46785 - "Winged helix" DNA-binding domain
144074 - E2F-DP heterodimerization region | 0.00586 | Inherited |
101288,50156
101288 - L27 domain
50156 - PDZ domain-like | 0.00586 | Inherited |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.02225 | Inherited |
47090,55486
47090 - PGBD-like
55486 - Metalloproteases ("zincins"), catalytic domain | 0.1048 | Inherited |
47413,46689
47413 - lambda repressor-like DNA-binding domains
46689 - Homeodomain-like | 0.1338 | Inherited |
(show details)
Supra-domains annotated to this MP term (Not in SPMP)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,90193,90193
57196 - EGF/Laminin
90193 - Notch domain
90193 - Notch domain | 0 | DIRECT |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.000001842 | DIRECT |
101288,50156,50044
101288 - L27 domain
50156 - PDZ domain-like
50044 - SH3-domain | 0.0003718 | DIRECT |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.0004065 | DIRECT |
81296,81296,81296
81296 - E set domains
81296 - E set domains
81296 - E set domains | 0.00166 | INHERITED FROM: abnormal retinal neuronal layer morphology || abnormal amacrine cell morphology |
55781,55781,109604
55781 - GAF domain-like
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.003132 | INHERITED FROM: retinal photoreceptor degeneration || abnormal retinal neuronal layer morphology || abnormal retinal photoreceptor morphology || abnormal retinal photoreceptor layer morphology || abnormal retinal layer morphology || decreased retinal photoreceptor cell number |
49899,57196,57196
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.009586 | INHERITED FROM: abnormal retinal ganglion layer morphology || abnormal retinal bipolar cell morphology || abnormal amacrine cell morphology |
57424,57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.01751 | INHERITED FROM: abnormal retinal pigment epithelium morphology |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57196,90193,90193
57196 - EGF/Laminin
90193 - Notch domain
90193 - Notch domain | 0 | Direct |
57196,57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.000001842 | Direct |
101288,50156,50044
101288 - L27 domain
50156 - PDZ domain-like
50044 - SH3-domain | 0.0003718 | Direct |
48726,48726,49265
48726 - Immunoglobulin
48726 - Immunoglobulin
49265 - Fibronectin type III | 0.0004065 | Direct |
81296,81296,81296
81296 - E set domains
81296 - E set domains
81296 - E set domains | 0.00166 | Inherited |
55781,55781,109604
55781 - GAF domain-like
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.003132 | Inherited |
49899,57196,57196
49899 - Concanavalin A-like lectins/glucanases
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.009586 | Inherited |
57424,57424,57424
57424 - LDL receptor-like module
57424 - LDL receptor-like module
57424 - LDL receptor-like module | 0.01751 | 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.
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