Mammalian Phenotype (MP): abnormal forebrain 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)

Shortest distance to current term (+ for parents, - for children) MP term [MP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + 4: mammalian phenotype [MP:0000001] <29>

+ + + 3: nervous system phenotype [MP:0003631] <2> (98|128) (113|79|50)

+ + 2: abnormal nervous system morphology [MP:0003632] <17> (76|104) (91|64|47)

+ 1: abnormal brain morphology [MP:0002152] <24> (25|42) (35|24|14)

0: abnormal forebrain morphology [MP:0000783] <8> (18|26) (24|15|8)

- 1: abnormal diencephalon morphology [MP:0000830] <11> (4|5) (6|1|0)

- 1: abnormal telencephalon morphology [MP:0000787] <9> (15|22) (19|12|6)

- 1: abnormal limbic system morphology [MP:0004166] <6> (7|8) (9|5|2)

- 1: abnormal basal ganglion morphology [MP:0006007] <5> (2|4) (2|0|0)

- 1: abnormal forebrain development [MP:0003232] <2> (3|5) (3|1|0)

- 1: abnormal forebrain size [MP:0012137] <2> (0|0) (0|0|0)

- 1: absent forebrain [MP:0012136] (0|0) (0|0|0)

- 1: forebrain atrophy [MP:0012508] (0|0) (0|0|0)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Homeodomain-like	0.006095	Inherited
Doublecortin (DC)	0.0308	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.03873	Inherited
lambda repressor-like DNA-binding domains	0.06545	Inherited
SH3-domain	0.1111	Inherited
Nuclear receptor ligand-binding domain	0.1226	Inherited
HLH, helix-loop-helix DNA-binding domain	0.1513	Inherited
Sema domain	0.1643	Inherited
SAP domain	0.1888	Inherited
Plexin repeat	0.2238	Inherited
Composite domain of metallo-dependent hydrolases	0.2261	Inherited
Metallo-dependent hydrolases	0.2261	Inherited
cAMP-binding domain-like	0.3206	Inherited
Cupredoxins	0.4458	Inherited
EGF/Laminin	0.5999	Inherited
Family A G protein-coupled receptor-like	0.7627	Inherited
Growth factor receptor domain	0.838	Inherited

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Other IPT/TIG domains	0	Direct
Hypoxia-inducible factor Hif2a, C-terminal domain	0.0007946	Direct
beta-glycanases	0.00195	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.00195	Inherited
Enabled/VASP homology 1 domain (EVH1 domain)	0.01907	Inherited
Doublecortin (DC)	0.02481	Inherited
Homeodomain	0.0267	Inherited
Ngr ectodomain-like	0.04822	Inherited
SH3-domain	0.104	Inherited
Nuclear receptor ligand-binding domain	0.109	Inherited
Nuclear receptor	0.109	Inherited
HLH, helix-loop-helix DNA-binding domain	0.1425	Inherited
Sema domain	0.1467	Inherited
SAP domain	0.1729	Inherited
cAMP-binding domain	0.1839	Inherited
Ephrin receptor ligand binding domain	0.2009	Inherited
Hydantoinase (dihydropyrimidinase)	0.2009	Inherited
Hydantoinase (dihydropyrimidinase), catalytic domain	0.2009	Inherited
Ephrin ectodomain	0.2009	Inherited
Plexin repeat	0.2061	Inherited
Voltage-gated potassium channels	0.3494	Inherited
Phosphotyrosine-binding domain (PTB)	0.3536	Inherited
SAM (sterile alpha motif) domain	0.3536	Inherited
EGF-type module	0.591	Inherited
Rhodopsin-like	0.8351	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)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Supra-domain (including individual superfamily)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Vasodilator-stimulated phosphoprotein, VASP, tetramerisation domain	0	Direct
Homeodomain-like	0.00369	Inherited
Doublecortin (DC)	0.021	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.02679	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.03297	Inherited
lambda repressor-like DNA-binding domains	0.04755	Inherited
SH3-domain	0.08507	Inherited
Nuclear receptor ligand-binding domain	0.09472	Inherited
HLH, helix-loop-helix DNA-binding domain	0.1199	Inherited
Sema domain	0.1312	Inherited
L domain-like	0.1417	Inherited
SAP domain	0.1531	Inherited
GTPase activation domain, GAP	0.1623	Inherited
Plexin repeat	0.1853	Inherited
Metallo-dependent hydrolases	0.1875	Inherited
Composite domain of metallo-dependent hydrolases	0.1875	Inherited
Glutamine synthetase/guanido kinase	0.2622	Inherited
cAMP-binding domain-like	0.2765	Inherited
Cupredoxins	0.3981	Inherited
E set domains	0.4416	Inherited
Voltage-gated potassium channels	0.4502	Inherited
EGF/Laminin	0.5545	Inherited
Family A G protein-coupled receptor-like	0.7251	Inherited
Growth factor receptor domain	0.8061	Inherited

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module	0	Direct
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin	0.0001189	Direct
48452,81901 48452 - TPR-like 81901 - HCP-like	0.001579	Inherited
57184,63825 57184 - Growth factor receptor domain 63825 - YWTD domain	0.002785	Inherited
57424,57184 57424 - LDL receptor-like module 57184 - Growth factor receptor domain	0.002785	Inherited
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.005356	Inherited
89837,89837 89837 - Doublecortin (DC) 89837 - Doublecortin (DC)	0.021	Inherited
52058,48726 52058 - L domain-like 48726 - Immunoglobulin	0.1057	Inherited
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.1312	Inherited
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain	0.1875	Inherited
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases	0.1875	Inherited
51338,51556 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases	0.1875	Inherited
81296,81296 81296 - E set domains 81296 - E set domains	0.2394	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.5567	Inherited
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0.6943	Inherited

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
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
57424,57184,63825 57424 - LDL receptor-like module 57184 - Growth factor receptor domain 63825 - YWTD domain	0.001087	Inherited
57424,57424,57184 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57184 - Growth factor receptor domain	0.001087	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.05879	Inherited
51338,51556,51338 51338 - Composite domain of metallo-dependent hydrolases 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases	0.1875	Inherited
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0.2394	Inherited
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0.6943	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)

SEARCH

BROWSE

TOOLS

ABOUT

HELP

Mammalian Phenotype (MP): abnormal forebrain morphology

Superfamily

Family

Supra-domain (including individual superfamily)