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Phenotypic Abnormality (PA): Neoplasm by anatomical site 
(show info)
Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype 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. Biomedical ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology 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 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 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 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 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 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 displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology 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 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 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.
- UniProtKB KeyWords (KW) Ontology 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).
- CTD Diseases (CD) Ontology CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
- CTD Chemicals (CC) Ontology CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).
Jump to [ Top · Hierarchy · Annotations ]
Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
Jump to [ Top · Hierarchy ]
Family( show details)
Highlighted in gray are those with FDR_all>0.001
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| DNA gyrase/MutL, second domain | 0 | DIRECT |
| DIX domain | 0 | DIRECT |
| DNA gyrase/MutL, N-terminal domain | 0 | DIRECT |
| DNA repair protein MutS, domain III | 0.008718 | INHERITED FROM: Malignant neoplasm of the central nervous system || Glioma || Neoplasm of the nervous system || Neoplasm of the rectum || Colon cancer || Intestinal polyp || Neoplasm of the large intestine || Neoplasm of the endocrine system || Neoplasm of the skin || Astrocytoma || Neoplasm of the stomach || Neoplasm of the genitourinary tract || Ovarian neoplasm || Neoplasm of the colon || Endometrial carcinoma || Neoplasm of the gastrointestinal tract || Gonadal neoplasm || Neoplasm of the thyroid gland || Intestinal polyposis || Neoplasm of the central nervous system || Uterine neoplasm |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.008718 | INHERITED FROM: Neoplasm of the gastrointestinal tract |
| Sema domain | 0.0139 | INHERITED FROM: Neoplasm of the thyroid gland |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.03577 | INHERITED FROM: Neoplasm of the breast || Breast carcinoma |
| POU-specific domain | 0.05219 | INHERITED FROM: Urinary tract neoplasm |
| Ras-binding domain, RBD | 0.05219 | INHERITED FROM: Malignant neoplasm of the central nervous system || Neuroblastoma || Neoplasm of the nervous system || Neuroblastic tumor || Neoplasm of the central nervous system |
| Plexin repeat | 0.07694 | INHERITED FROM: Neoplasm of the thyroid gland |
| FHA domain | 0.08301 | INHERITED FROM: Malignant neoplasm of the central nervous system |
| RING finger domain, C3HC4 | 0.097 | INHERITED FROM: Breast carcinoma |
| DEATH domain, DD | 0.1005 | INHERITED FROM: Lymphoma |
| Laminin-type module | 0.1821 | INHERITED FROM: Squamous cell carcinoma || Squamous cell carcinoma of the skin |
| Nuclear receptor ligand-binding domain | 0.2156 | INHERITED FROM: Testicular gonadoblastoma || Neoplasm of the male external genitalia || Testicular neoplasm |
| Intermediate filament protein, coiled coil region | 0.2284 | INHERITED FROM: Verrucae || Neoplasm of the skin || Squamous cell carcinoma of the skin |
| ABC transporter ATPase domain-like | 0.7595 | INHERITED FROM: Astrocytoma || Endometrial carcinoma |
| RecA protein-like (ATPase-domain) | 0.8164 | INHERITED FROM: Neoplasm of the breast || Myelodysplasia || Breast carcinoma || Primary peritoneal carcinoma |
| Protein kinases, catalytic subunit | 1 | INHERITED FROM: Hemangioma |
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| DNA gyrase/MutL, second domain | 0 | Direct |
| DIX domain | 0 | Direct |
| DNA gyrase/MutL, N-terminal domain | 0 | Direct |
| DNA repair protein MutS, domain III | 0.008718 | Inherited |
| Rel/Dorsal transcription factors, DNA-binding domain | 0.008718 | Inherited |
| Sema domain | 0.0139 | Inherited |
| Phoshoinositide 3-kinase (PI3K), catalytic domain | 0.03577 | Inherited |
| POU-specific domain | 0.05219 | Inherited |
| Ras-binding domain, RBD | 0.05219 | Inherited |
| Plexin repeat | 0.07694 | Inherited |
| FHA domain | 0.08301 | Inherited |
| RING finger domain, C3HC4 | 0.097 | Inherited |
| DEATH domain, DD | 0.1005 | Inherited |
| Laminin-type module | 0.1821 | Inherited |
| Nuclear receptor ligand-binding domain | 0.2156 | Inherited |
| Intermediate filament protein, coiled coil region | 0.2284 | Inherited |
| ABC transporter ATPase domain-like | 0.7595 | Inherited |
| RecA protein-like (ATPase-domain) | 0.8164 | Inherited |
| Protein kinases, catalytic subunit | 1 | Inherited |
LINKTO: Domain2BO Download and Domain2BO Algorithm
Plot distribution on species Tree Of Life (sTOL) for Superfamily and/or Family domains annotated by this HP 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.
Plot distribution on species Tree Of Life (sTOL) for single supra-domains annotated by this HP term
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Plot tree as:
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Download Newick format tree:
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Browsing in TREE OF LIFE:
|
( 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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> BO Hierarchy > Neoplasm by anatomical site
