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Phenotypic Abnormality (PA): Abnormality of blood and blood-forming tissues 
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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).
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Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
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Family( show details)
Highlighted in gray are those with FDR_all>0.001
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| Proteasome subunits | 0 | DIRECT |
| Globins | 0 | DIRECT |
| Fibrinogen coiled-coil and central regions | 0 | DIRECT |
| Eukaryotic proteases | 0.000001139 | DIRECT |
| SH2 domain | 0.00003831 | DIRECT |
| GLA-domain | 0.001407 | INHERITED FROM: Post-partum hemorrhage || Abnormal prothrombin time || Deep venous thrombosis || Internal hemorrhage || Prolonged prothrombin time || Abnormality of the coagulation cascade || Abnormal bleeding || Venous thrombosis || Prolonged bleeding following procedure || Abnormality of coagulation || Joint hemorrhage |
| DEATH domain, DD | 0.006967 | INHERITED FROM: Subcutaneous hemorrhage || Lymphoma |
| Complement control module/SCR domain | 0.008797 | INHERITED FROM: Anemia due to reduced life span of red cells || Microangiopathic hemolytic anemia || Schistocytosis || Reticulocytosis || Abnormal platelet count |
| Ras GEF | 0.01096 | INHERITED FROM: Abnormal thrombocyte morphology || Abnormal bleeding |
| DNA gyrase/MutL, second domain | 0.01096 | INHERITED FROM: Internal hemorrhage || Abnormal bleeding || Gastrointestinal hemorrhage |
| DNA gyrase/MutL, N-terminal domain | 0.01096 | INHERITED FROM: Internal hemorrhage || Abnormal bleeding || Gastrointestinal hemorrhage |
| Pyrin domain, PYD | 0.01096 | INHERITED FROM: Abnormal leukocyte count || Abnormal leukocyte morphology || Leukocytosis |
| Kringle modules | 0.02868 | INHERITED FROM: Deep venous thrombosis || Abnormality of coagulation |
| ABC transporter ATPase domain-like | 0.02924 | INHERITED FROM: Stomatocytosis || Episodic hemolytic anemia |
| Nitrogenase iron protein-like | 0.03468 | INHERITED FROM: Abnormality of multiple cell lineages in the bone marrow || Abnormal leukocyte count || Lymphopenia || Pancytopenia |
| Transcription factor STAT-4 N-domain | 0.03468 | INHERITED FROM: Leukopenia || Thrombocytopenia || Neutropenia || Abnormal neutrophil count || Abnormal leukocyte count || Abnormal platelet count || Abnormal thrombocyte morphology |
| STAT DNA-binding domain | 0.03468 | INHERITED FROM: Leukopenia || Thrombocytopenia || Neutropenia || Abnormal neutrophil count || Abnormal leukocyte count || Abnormal platelet count || Abnormal thrombocyte morphology |
| STAT | 0.03468 | INHERITED FROM: Leukopenia || Thrombocytopenia || Neutropenia || Abnormal neutrophil count || Abnormal leukocyte count || Abnormal platelet count || Abnormal thrombocyte morphology |
| MHC antigen-recognition domain | 0.05472 | INHERITED FROM: Venous thrombosis |
| Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) | 0.07114 | INHERITED FROM: Bruising susceptibility |
| BEACH domain | 0.07646 | INHERITED FROM: Abnormality of bone marrow cell morphology || Abnormality of multiple cell lineages in the bone marrow |
| Fibrinogen C-terminal domain-like | 0.09926 | INHERITED FROM: Abnormality of the common coagulation pathway || Abnormality of circulating fibrinogen || Internal hemorrhage || Venous thrombosis |
| 28-residue LRR | 0.09926 | INHERITED FROM: Leukocytosis |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.1191 | INHERITED FROM: Abnormal thrombocyte morphology |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain | 0.1379 | INHERITED FROM: Leukopenia |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.1718 | INHERITED FROM: Intracranial hemorrhage |
| Integrin domains | 0.1718 | INHERITED FROM: Subarachnoid hemorrhage || Spontaneous hematomas || Intracranial hemorrhage || Cephalohematoma || Petechiae || Ecchymosis || Purpura || Neonatal alloimmune thrombocytopenia || Macular purpura || Melena |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.1718 | INHERITED FROM: Intracranial hemorrhage |
| VWC domain | 0.2081 | INHERITED FROM: Bruising susceptibility |
| RecA protein-like (ATPase-domain) | 0.2319 | INHERITED FROM: Sideroblastic anemia || Pyridoxine-responsive sideroblastic anemia || Myelodysplasia |
| Second domain of FERM | 0.2521 | INHERITED FROM: Cerebral hemorrhage |
| G proteins | 0.2826 | INHERITED FROM: Abnormal platelet function |
| Transglutaminase core | 0.2843 | INHERITED FROM: Abnormality of the common coagulation pathway || Abnormality of the coagulation cascade |
| V set domains (antibody variable domain-like) | 0.3015 | INHERITED FROM: Abnormal lymphocyte morphology |
| Ngr ectodomain-like | 0.964 | INHERITED FROM: Abnormal platelet aggregation || Abnormal megakaryocyte morphology || Macrothrombocytopenia || Spontaneous, recurrent epistaxis || Spontaneous hematomas || Impaired platelet aggregation || Prolonged bleeding after surgery || Prolonged bleeding time || Giant platelets || Prolonged bleeding after dental extraction || Hematemesis || Menorrhagia || Decreased platelet glycoprotein Ib-IX-V || Impaired ristocetin-induced platelet aggregation || Abnormal platelet membrane protein expression || Abnormality of von Willebrand factor || Abnormal platelet volume || Prolonged bleeding following procedure || Increased mean platelet volume |
LINKTO: Domain2BO Download and Domain2BO Algorithm
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Supra-domain (Single)( show details)
Highlighted in gray are those with FDR>0.001
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
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Supra-domain (Duplex) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57630,57196
57630 - GLA-domain
57196 - EGF/Laminin | 0 | DIRECT |
49562,48350
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48350 - GTPase activation domain, GAP | 0 | DIRECT |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.0001093 | DIRECT |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.0003562 | DIRECT |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.0006806 | DIRECT |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.0009696 | DIRECT |
57440,50494
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0.001114 | INHERITED FROM: Deep venous thrombosis || Venous thrombosis |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0.009418 | INHERITED FROM: Internal hemorrhage || Abnormal bleeding || Gastrointestinal hemorrhage |
47986,52540
47986 - DEATH domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.009418 | INHERITED FROM: Leukocytosis |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.02079 | INHERITED FROM: Anemia of inadequate production |
50729,81837
50729 - PH domain-like
81837 - BEACH domain | 0.02533 | INHERITED FROM: Abnormal thrombocyte morphology || Abnormal platelet count || Abnormality of bone marrow cell morphology || Thrombocytopenia || Abnormality of multiple cell lineages in the bone marrow |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.0296 | INHERITED FROM: Abnormality of coagulation |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.03018 | INHERITED FROM: Abnormal leukocyte count || Abnormal thrombocyte morphology || Abnormal platelet count || Neutropenia || Leukopenia || Abnormal neutrophil count || Thrombocytopenia |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.03018 | INHERITED FROM: Abnormal leukocyte count || Abnormal thrombocyte morphology || Abnormal platelet count || Neutropenia || Leukopenia || Abnormal neutrophil count || Thrombocytopenia |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.03018 | INHERITED FROM: Abnormal leukocyte count || Abnormal thrombocyte morphology || Abnormal platelet count || Neutropenia || Leukopenia || Abnormal neutrophil count || Thrombocytopenia |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.04675 | INHERITED FROM: Venous thrombosis |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
57630,57196
57630 - GLA-domain
57196 - EGF/Laminin | 0 | Direct |
49562,48350
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
48350 - GTPase activation domain, GAP | 0 | Direct |
55550,56112
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0.0001093 | Direct |
50044,55550
50044 - SH3-domain
55550 - SH2 domain | 0.0003562 | Direct |
57586,57586
57586 - TNF receptor-like
57586 - TNF receptor-like | 0.0006806 | Direct |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.0009696 | Direct |
57440,50494
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0.001114 | Inherited |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0.009418 | Inherited |
47986,52540
47986 - DEATH domain
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.009418 | Inherited |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.02079 | Inherited |
50729,81837
50729 - PH domain-like
81837 - BEACH domain | 0.02533 | Inherited |
57440,57440
57440 - Kringle-like
57440 - Kringle-like | 0.0296 | Inherited |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.03018 | Inherited |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.03018 | Inherited |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.03018 | Inherited |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.04675 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm
Jump to [ Top · Hierarchy ]
Supra-domain (Triple) in N- to C-terminal order( show details)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.00003269 | DIRECT |
57440,57440,50494
57440 - Kringle-like
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0.009418 | INHERITED FROM: Abnormality of coagulation |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.03018 | INHERITED FROM: Abnormal leukocyte count || Abnormal thrombocyte morphology || Abnormal platelet count || Neutropenia || Leukopenia || Abnormal neutrophil count || Thrombocytopenia |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.03018 | INHERITED FROM: Abnormal leukocyte count || Abnormal thrombocyte morphology || Abnormal platelet count || Neutropenia || Leukopenia || Abnormal neutrophil count || Thrombocytopenia |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
50044,55550,56112
50044 - SH3-domain
55550 - SH2 domain
56112 - Protein kinase-like (PK-like) | 0 | Direct |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.00003269 | Direct |
57440,57440,50494
57440 - Kringle-like
57440 - Kringle-like
50494 - Trypsin-like serine proteases | 0.009418 | Inherited |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.03018 | Inherited |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.03018 | Inherited |
LINKTO: Supra-domain2BO Download and Supra-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:
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( 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 > Abnormality of blood and blood-forming tissues
