Mammalian Phenotype (MP): neoplasm

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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
Mouse Phenotype (MP) Ontology (MP)
MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
Worm Phenotype (WP) Ontology (WP)
WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
Yeast Phenotype (YP) Ontology (YP)
Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
Fly Phenotype (FP) Ontology (FP)
FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
Fly Anatomy (FA) Ontology (FA)
FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
Zebrafish Anatomy (ZA) Ontology (ZA)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
Arabidopsis Plant Ontology (AP) Ontology (AP)
As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
Enzyme Commission (EC) Ontology (EC)
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

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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)

+ 1: mammalian phenotype [MP:0000001] <29>

0: neoplasm [MP:0002006] <2> (32|37) (38|18|7)

- 1: altered tumor pathology [MP:0010639] <4> (9|11) (10|8|5)

- 1: altered tumor susceptibility [MP:0002166] <3> (25|29) (30|11|3)

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

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
p53 tetramerization domain	0	Direct
Protein kinase-like (PK-like)	0.000000006774	Direct
SMAD MH1 domain	0.00003976	Direct
4-helical cytokines	0.000102	Direct
DNA/RNA polymerases	0.0001514	Direct
Bcl-2 inhibitors of programmed cell death	0.001518	Inherited
SMAD/FHA domain	0.001868	Inherited
Restriction endonuclease-like	0.002	Inherited
SPOC domain-like	0.002	Inherited
DNA-glycosylase	0.002	Inherited
Cyclin-like	0.002703	Inherited
Nucleic acid-binding proteins	0.003743	Inherited
SAND domain-like	0.006443	Inherited
DNA repair protein MutS, domain III	0.006443	Inherited
Notch domain	0.006443	Inherited
RING/U-box	0.009593	Inherited
PGBD-like	0.01398	Inherited
Integrin beta tail domain	0.02363	Inherited
STAT	0.02363	Inherited
Transcription factor STAT-4 N-domain	0.02363	Inherited
Putative DNA-binding domain	0.02363	Inherited
Hemopexin-like domain	0.02895	Inherited
p53-like transcription factors	0.03167	Inherited
BRCT domain	0.04278	Inherited
Kringle-like	0.09072	Inherited
CCCH zinc finger	0.1088	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.1934	Inherited
SET domain	0.1999	Inherited
ARM repeat	0.2128	Inherited
Metalloproteases ("zincins"), catalytic domain	0.2244	Inherited
Ubiquitin-like	0.5116	Inherited
Intermediate filament protein, coiled coil region	0.5648	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
p53 DNA-binding domain-like	0	Direct
p53 tetramerization domain	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Protein kinases, catalytic subunit	0.0000004534	Direct
SMAD MH1 domain	0.00002984	Direct
DNA replication initiator (cdc21/cdc54) N-terminal domain	0.00002984	Direct
SMAD domain	0.00002984	Direct
DNA polymerase I	0.0009854	Direct
Bcl-2 inhibitors of programmed cell death	0.001208	Inherited
XPF/Rad1/Mus81 nuclease	0.001482	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.001834	Inherited
Pointed domain	0.002529	Inherited
L domain	0.002529	Inherited
Matrix metalloproteases, catalytic domain	0.004361	Inherited
Notch domain	0.005016	Inherited
DNA repair protein MutS, domain III	0.005016	Inherited
Interferons/interleukin-10 (IL-10)	0.009034	Inherited
Short-chain cytokines	0.009838	Inherited
MMP N-terminal domain	0.01246	Inherited
p120GAP domain-like	0.01423	Inherited
Integrin beta tail domain	0.01966	Inherited
STAT DNA-binding domain	0.01966	Inherited
Single strand DNA-binding domain, SSB	0.01966	Inherited
Transcription factor STAT-4 N-domain	0.01966	Inherited
STAT	0.01966	Inherited
Pyrin domain, PYD	0.01966	Inherited
Forkhead DNA-binding domain	0.0227	Inherited
Hemopexin-like domain	0.02639	Inherited
DnaQ-like 3'-5' exonuclease	0.02915	Inherited
Integrin beta EGF-like domains	0.03072	Inherited
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.046	Inherited
Histone lysine methyltransferases	0.0728	Inherited
CCCH zinc finger	0.09941	Inherited
FHA domain	0.1678	Inherited
Phosphotyrosine-binding domain (PTB)	0.5529	Inherited
Intermediate filament protein, coiled coil region	0.574	Inherited
ABC transporter ATPase domain-like	0.5987	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
p53 tetramerization domain	0	Direct
Protein kinase-like (PK-like)	0.000000002564	Direct
SMAD MH1 domain	0.00001847	Direct
4-helical cytokines	0.00004941	Direct
DNA/RNA polymerases	0.00007561	Direct
Bcl-2 inhibitors of programmed cell death	0.0008508	Direct
SMAD/FHA domain	0.001059	Inherited
SPOC domain-like	0.001136	Inherited
Restriction endonuclease-like	0.001136	Inherited
DNA-glycosylase	0.001136	Inherited
Cyclin-like	0.001557	Inherited
Nucleic acid-binding proteins	0.002195	Inherited
SAND domain-like	0.003923	Inherited
Notch domain	0.003923	Inherited
DNA repair protein MutS, domain III	0.003923	Inherited
RING/U-box	0.005976	Inherited
PGBD-like	0.008951	Inherited
Chromo domain-like	0.009515	Inherited
Snake toxin-like	0.01415	Inherited
Integrin beta tail domain	0.01571	Inherited
STAT	0.01571	Inherited
Putative DNA-binding domain	0.01571	Inherited
Transcription factor STAT-4 N-domain	0.01571	Inherited
Hemopexin-like domain	0.0196	Inherited
p53-like transcription factors	0.02164	Inherited
BRCT domain	0.02985	Inherited
Cysteine-rich domain	0.04284	Inherited
ENTH/VHS domain	0.05114	Inherited
Kringle-like	0.06778	Inherited
Ribonuclease H-like	0.06823	Inherited
Leucine zipper domain	0.08149	Inherited
CCCH zinc finger	0.083	Inherited
C2 domain (Calcium/lipid-binding domain, CaLB)	0.1574	Inherited
SET domain	0.1633	Inherited
ARM repeat	0.175	Inherited
Metalloproteases ("zincins"), catalytic domain	0.186	Inherited
Ubiquitin-like	0.4642	Inherited
Intermediate filament protein, coiled coil region	0.5183	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	Direct
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.00002261	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0.001136	Inherited
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.001698	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.001879	Inherited
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.001879	Inherited
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like)	0.003858	Inherited
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.003858	Inherited
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0.003923	Inherited
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.008951	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.01571	Inherited
53300,69179 53300 - vWA-like 69179 - Integrin domains	0.01571	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.01571	Inherited
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0.01571	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.01571	Inherited
51045,51045 51045 - WW domain 51045 - WW domain	0.03097	Inherited
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.0633	Inherited
50729,50729 50729 - PH domain-like 50729 - PH domain-like	0.1777	Inherited

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0.001136	Inherited
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.001879	Inherited
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.003923	Inherited
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.01571	Inherited
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0.01571	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.01571	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1023	Inherited

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Mammalian Phenotype (MP): neoplasm

Superfamily

Family

Supra-domain (including individual superfamily)