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Phenotypic Abnormality (PA): Abnormality of the genitourinary system
(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: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this HP term (SDHP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Zn-finger domain of Sec23/24 | 0 | DIRECT |
| Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain | 0 | DIRECT |
| DNA repair protein MutS, domain III | 0 | DIRECT |
| DNA gyrase/MutL, second domain | 0 | DIRECT |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0 | DIRECT |
| alpha-Amylases, C-terminal beta-sheet domain | 0 | DIRECT |
| Lamin A/C globular tail domain | 0 | DIRECT |
| Cytochrome b5 | 0 | DIRECT |
| ARID domain | 0 | DIRECT |
| beta-glycanases | 0 | DIRECT |
| Diacylglycerol kinase-like | 0 | DIRECT |
| Cystathionine synthase-like | 0 | DIRECT |
| Smc hinge domain | 0 | DIRECT |
| XPF/Rad1/Mus81 nuclease | 0 | DIRECT |
| Insulin-like | 0 | DIRECT |
| DIX domain | 0 | DIRECT |
| HCDH C-domain-like | 0 | DIRECT |
| Dual specificity phosphatase-like | 0 | DIRECT |
| Integrin alpha N-terminal domain | 0 | DIRECT |
| Dimeric isocitrate & isopropylmalate dehydrogenases | 0 | DIRECT |
| Phosphoribosyltransferases (PRTases) | 0 | DIRECT |
| Fibrinogen coiled-coil and central regions | 0 | DIRECT |
| DNA gyrase/MutL, N-terminal domain | 0 | DIRECT |
| DNA polymerase I | 0 | DIRECT |
| Sec63 N-terminal domain | 0 | DIRECT |
| IF2B-like | 0 | DIRECT |
| TBP-associated factors, TAFs | 0 | DIRECT |
| PHD domain | 0.001068 | INHERITED FROM: Abnormal ureter physiology || Abnormality of male external genitalia || Cryptorchidism |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.01036 | INHERITED FROM: Aciduria || Abnormality of urine homeostasis || Dicarboxylic aciduria || Abnormality of the urinary system physiology |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.01036 | INHERITED FROM: Aciduria || Abnormality of urine homeostasis || Dicarboxylic aciduria || Abnormality of the urinary system physiology |
| Bromodomain | 0.03684 | INHERITED FROM: Abnormal testis morphology || Cryptorchidism |
| Arylsulfatase | 0.03804 | INHERITED FROM: Urinary glycosaminoglycan excretion |
| Histone lysine methyltransferases | 0.03804 | INHERITED FROM: Hypospadias || Abnormality of the male genitalia || Abnormal external genitalia || Abnormal ureter physiology || Displacement of the urethral meatus || Abnormal testis morphology || Abnormality of male external genitalia || Abnormality of the lower urinary tract || Cryptorchidism || Abnormal reproductive system morphology |
| RecA protein-like (ATPase-domain) | 0.03804 | INHERITED FROM: Bicornuate uterus || Prostate neoplasm || Recurrent urinary tract infections || Azoospermia || Decreased fertility in males || Absent testis || Abnormal spermatogenesis || Abnormal ureter morphology || Abnormality of the preputium || Abnormal uterus morphology || Abnormal prostate morphology || Hydroureter || Abnormality of the fallopian tube |
| BC N-terminal domain-like | 0.05109 | INHERITED FROM: Aciduria || Abnormality of the urinary system physiology |
| POU-specific domain | 0.05109 | INHERITED FROM: Urinary tract neoplasm |
| Transcription factor STAT-4 N-domain | 0.05109 | INHERITED FROM: Abnormal urine cytology |
| Crotonase-like | 0.05109 | INHERITED FROM: Aminoaciduria || Aciduria |
| STAT DNA-binding domain | 0.05109 | INHERITED FROM: Abnormal urine cytology |
| STAT | 0.05109 | INHERITED FROM: Abnormal urine cytology |
| BC ATP-binding domain-like | 0.05109 | INHERITED FROM: Aciduria || Abnormality of the urinary system physiology |
| CalX-beta domain | 0.08465 | INHERITED FROM: Abnormal vagina morphology |
| RING finger domain, C3HC4 | 0.09462 | INHERITED FROM: Prostate neoplasm || Abnormal prostate morphology |
| HMG-box | 0.09462 | INHERITED FROM: Abnormal testis morphology || Dilatation of the renal pelvis || Hypogonadotrophic hypogonadism |
| GAF domain | 0.1387 | INHERITED FROM: Hypogonadism |
| Extended AAA-ATPase domain | 0.1629 | INHERITED FROM: Abnormal size of the clitoris || Abnormality of the clitoris |
| Cytoplasmic domain of inward rectifier potassium channel | 0.1762 | INHERITED FROM: Abnormal urinary electrolyte concentration || Abnormal urine output || Polyuria |
| Actin/HSP70 | 0.1762 | INHERITED FROM: Abnormality of the ureter || Hydroureter |
| Noncollagenous (NC1) domain of collagen IV | 0.2039 | INHERITED FROM: Abnormal urine cytology || Abnormal renal corpuscle morphology || Nephritis || Abnormality of renal glomerulus morphology || Proteinuria || Diffuse glomerular basement membrane lamellation || Thickening of the glomerular basement membrane || Stage 5 chronic kidney disease || Hematuria || Renal insufficiency |
| Extracellular domain of cell surface receptors | 0.2039 | INHERITED FROM: Abnormality of the uterus |
| Homeodomain | 0.2044 | INHERITED FROM: Ureteropelvic junction obstruction |
| MHC antigen-recognition domain | 0.2059 | INHERITED FROM: Glomerulopathy || Abnormal nephron morphology |
| PDEase | 0.247 | INHERITED FROM: Hypogonadism || Abnormality of reproductive system physiology |
| WD40-repeat | 0.3017 | INHERITED FROM: Nephronophthisis || Abnormal renal medulla morphology |
| C1 set domains (antibody constant domain-like) | 0.3201 | INHERITED FROM: Glomerulopathy |
| ABC transporter ATPase domain-like | 0.3314 | INHERITED FROM: Endometrial carcinoma || Abnormality of the endometrium |
| Clc chloride channel | 0.341 | INHERITED FROM: Abnormal urinary electrolyte concentration |
| Chromo domain | 0.3685 | INHERITED FROM: Azoospermia || Abnormal spermatogenesis |
| Nuclear receptor | 0.3772 | INHERITED FROM: Primary amenorrhea |
| Nuclear receptor ligand-binding domain | 0.3847 | INHERITED FROM: Male pseudohermaphroditism || Abnormality of female internal genitalia || Testicular neoplasm || Female external genitalia in individual with 46,XY karyotype || Neoplasm of the male external genitalia || Primary amenorrhea || Polycystic ovaries || Testicular gonadoblastoma |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.404 | INHERITED FROM: Nephritis || Glomerulonephritis |
| Canonical RBD | 0.4067 | INHERITED FROM: Decreased fertility in males || Non-obstructive azoospermia || Male infertility || Oligospermia |
| Fibrinogen C-terminal domain-like | 0.4881 | INHERITED FROM: Menometrorrhagia |
| Mitochondrial carrier | 0.5106 | INHERITED FROM: Organic aciduria |
| Fibroblast growth factors (FGF) | 0.5984 | INHERITED FROM: Renal agenesis |
| Eukaryotic proteases | 0.6459 | INHERITED FROM: Abnormal urine output || Decreased urine output || Menorrhagia |
| Cytochrome P450 | 0.661 | INHERITED FROM: Abnormal urinary electrolyte concentration |
| Complement control module/SCR domain | 0.7373 | INHERITED FROM: Abnormal urine cytology || Hemolytic-uremic syndrome || Anuria || Abnormal urine output || Acute kidney injury || Abnormality of renal excretion || Decreased urine output || Renal insufficiency |
| Rhodopsin-like | 0.8108 | INHERITED FROM: Hypoplasia of the ovary || Aplasia/Hypoplasia of the ovary || Abnormal libido || Erectile abnormalities || Female sexual dysfunction |
| TNF-like | 0.9699 | INHERITED FROM: Nephritis || Glomerulonephritis |
| Ngr ectodomain-like | 0.9796 | INHERITED FROM: Macroscopic hematuria || Partially duplicated kidney || Renal duplication || Menorrhagia |
| Voltage-gated potassium channels | 0.9867 | INHERITED FROM: Polyuria |
| SCOP term | FDR (all) | Annotation (direct or inherited) |
| Zn-finger domain of Sec23/24 | 0 | Direct |
| Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain | 0 | Direct |
| DNA repair protein MutS, domain III | 0 | Direct |
| DNA gyrase/MutL, second domain | 0 | Direct |
| Formate/glycerate dehydrogenases, substrate-binding domain | 0 | Direct |
| alpha-Amylases, C-terminal beta-sheet domain | 0 | Direct |
| Lamin A/C globular tail domain | 0 | Direct |
| Cytochrome b5 | 0 | Direct |
| ARID domain | 0 | Direct |
| beta-glycanases | 0 | Direct |
| Diacylglycerol kinase-like | 0 | Direct |
| Cystathionine synthase-like | 0 | Direct |
| Smc hinge domain | 0 | Direct |
| XPF/Rad1/Mus81 nuclease | 0 | Direct |
| Insulin-like | 0 | Direct |
| DIX domain | 0 | Direct |
| HCDH C-domain-like | 0 | Direct |
| Dual specificity phosphatase-like | 0 | Direct |
| Integrin alpha N-terminal domain | 0 | Direct |
| Dimeric isocitrate & isopropylmalate dehydrogenases | 0 | Direct |
| Phosphoribosyltransferases (PRTases) | 0 | Direct |
| Fibrinogen coiled-coil and central regions | 0 | Direct |
| DNA gyrase/MutL, N-terminal domain | 0 | Direct |
| DNA polymerase I | 0 | Direct |
| Sec63 N-terminal domain | 0 | Direct |
| IF2B-like | 0 | Direct |
| TBP-associated factors, TAFs | 0 | Direct |
| PHD domain | 0.001068 | Inherited |
| Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.01036 | Inherited |
| Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.01036 | Inherited |
| Bromodomain | 0.03684 | Inherited |
| Arylsulfatase | 0.03804 | Inherited |
| Histone lysine methyltransferases | 0.03804 | Inherited |
| RecA protein-like (ATPase-domain) | 0.03804 | Inherited |
| BC N-terminal domain-like | 0.05109 | Inherited |
| POU-specific domain | 0.05109 | Inherited |
| Transcription factor STAT-4 N-domain | 0.05109 | Inherited |
| Crotonase-like | 0.05109 | Inherited |
| STAT DNA-binding domain | 0.05109 | Inherited |
| STAT | 0.05109 | Inherited |
| BC ATP-binding domain-like | 0.05109 | Inherited |
| CalX-beta domain | 0.08465 | Inherited |
| RING finger domain, C3HC4 | 0.09462 | Inherited |
| HMG-box | 0.09462 | Inherited |
| GAF domain | 0.1387 | Inherited |
| Extended AAA-ATPase domain | 0.1629 | Inherited |
| Cytoplasmic domain of inward rectifier potassium channel | 0.1762 | Inherited |
| Actin/HSP70 | 0.1762 | Inherited |
| Noncollagenous (NC1) domain of collagen IV | 0.2039 | Inherited |
| Extracellular domain of cell surface receptors | 0.2039 | Inherited |
| Homeodomain | 0.2044 | Inherited |
| MHC antigen-recognition domain | 0.2059 | Inherited |
| PDEase | 0.247 | Inherited |
| WD40-repeat | 0.3017 | Inherited |
| C1 set domains (antibody constant domain-like) | 0.3201 | Inherited |
| ABC transporter ATPase domain-like | 0.3314 | Inherited |
| Clc chloride channel | 0.341 | Inherited |
| Chromo domain | 0.3685 | Inherited |
| Nuclear receptor | 0.3772 | Inherited |
| Nuclear receptor ligand-binding domain | 0.3847 | Inherited |
| Protein kinase cysteine-rich domain (cys2, phorbol-binding domain) | 0.404 | Inherited |
| Canonical RBD | 0.4067 | Inherited |
| Fibrinogen C-terminal domain-like | 0.4881 | Inherited |
| Mitochondrial carrier | 0.5106 | Inherited |
| Fibroblast growth factors (FGF) | 0.5984 | Inherited |
| Eukaryotic proteases | 0.6459 | Inherited |
| Cytochrome P450 | 0.661 | Inherited |
| Complement control module/SCR domain | 0.7373 | Inherited |
| Rhodopsin-like | 0.8108 | Inherited |
| TNF-like | 0.9699 | Inherited |
| Ngr ectodomain-like | 0.9796 | Inherited |
| Voltage-gated potassium channels | 0.9867 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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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)
(show details)
Supra-domains annotated to this HP term (SPHO level: Least Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
53098,56672
53098 - Ribonuclease H-like
56672 - DNA/RNA polymerases | 0 | DIRECT |
52980,47781
52980 - Restriction endonuclease-like
47781 - RuvA domain 2-like | 0 | DIRECT |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0 | DIRECT |
82919,53300
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 0 | DIRECT |
57903,51197
57903 - FYVE/PHD zinc finger
51197 - Clavaminate synthase-like | 0 | DIRECT |
52540,46785
52540 - P-loop containing nucleoside triphosphate hydrolases
46785 - "Winged helix" DNA-binding domain | 0 | DIRECT |
52096,52096
52096 - ClpP/crotonase
52096 - ClpP/crotonase | 0 | DIRECT |
51735,55347
51735 - NAD(P)-binding Rossmann-fold domains
55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0 | DIRECT |
-7,56112
-7 - CATH
56112 - Protein kinase-like (PK-like) | 0 | DIRECT |
48334,52540
48334 - DNA repair protein MutS, domain III
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0 | DIRECT |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0 | DIRECT |
52113,52113
52113 - BRCT domain
52113 - BRCT domain | 0 | DIRECT |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.02244 | INHERITED FROM: Spastic/hyperactive bladder |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.04835 | INHERITED FROM: Abnormal urine cytology |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.04835 | INHERITED FROM: Abnormal urine cytology |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.04835 | INHERITED FROM: Abnormal urine cytology |
50978,50978
50978 - WD40 repeat-like
50978 - WD40 repeat-like | 0.05564 | INHERITED FROM: Nephronophthisis || Abnormal renal medulla morphology |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.07208 | INHERITED FROM: Hydroureter |
56645,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.08052 | INHERITED FROM: Abnormality of the urinary system physiology || Aciduria || Dicarboxylic aciduria |
55781,109604
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.1339 | INHERITED FROM: Hypogonadism |
57903,47370
57903 - FYVE/PHD zinc finger
47370 - Bromodomain | 0.1339 | INHERITED FROM: Functional abnormality of the bladder || Abnormality of the bladder |
55781,55781
55781 - GAF domain-like
55781 - GAF domain-like | 0.1339 | INHERITED FROM: Hypogonadism |
81324,81296
81324 - Voltage-gated potassium channels
81296 - E set domains | 0.1691 | INHERITED FROM: Polyuria || Abnormality of renal excretion || Abnormal urine output || Abnormal urinary electrolyte concentration |
57903,57903
57903 - FYVE/PHD zinc finger
57903 - FYVE/PHD zinc finger | 0.197 | INHERITED FROM: Dilatation of the renal pelvis |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.1976 | INHERITED FROM: Abnormal nephron morphology || Glomerulopathy |
56436,56436
56436 - C-type lectin-like
56436 - C-type lectin-like | 0.4643 | INHERITED FROM: Renal insufficiency || Abnormal urine cytology || Diffuse glomerular basement membrane lamellation || Abnormal renal corpuscle morphology || Stage 5 chronic kidney disease || Thickening of the glomerular basement membrane || Nephritis || Hematuria || Abnormality of renal glomerulus morphology |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.4951 | INHERITED FROM: Renal insufficiency || Abnormal urine cytology || Decreased urine output || Abnormality of renal excretion || Abnormal urine output || Anuria || Hemolytic-uremic syndrome || Acute kidney injury |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
53098,56672
53098 - Ribonuclease H-like
56672 - DNA/RNA polymerases | 0 | Direct |
52980,47781
52980 - Restriction endonuclease-like
47781 - RuvA domain 2-like | 0 | Direct |
69179,69179
69179 - Integrin domains
69179 - Integrin domains | 0 | Direct |
82919,53300
82919 - Zn-finger domain of Sec23/24
53300 - vWA-like | 0 | Direct |
57903,51197
57903 - FYVE/PHD zinc finger
51197 - Clavaminate synthase-like | 0 | Direct |
52540,46785
52540 - P-loop containing nucleoside triphosphate hydrolases
46785 - "Winged helix" DNA-binding domain | 0 | Direct |
52096,52096
52096 - ClpP/crotonase
52096 - ClpP/crotonase | 0 | Direct |
51735,55347
51735 - NAD(P)-binding Rossmann-fold domains
55347 - Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0 | Direct |
-7,56112
-7 - CATH
56112 - Protein kinase-like (PK-like) | 0 | Direct |
48334,52540
48334 - DNA repair protein MutS, domain III
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
55874,54211
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like | 0 | Direct |
69318,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains | 0 | Direct |
52113,52113
52113 - BRCT domain
52113 - BRCT domain | 0 | Direct |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.02244 | Inherited |
47655,49417
47655 - STAT
49417 - p53-like transcription factors | 0.04835 | Inherited |
49417,55550
49417 - p53-like transcription factors
55550 - SH2 domain | 0.04835 | Inherited |
48092,47655
48092 - Transcription factor STAT-4 N-domain
47655 - STAT | 0.04835 | Inherited |
50978,50978
50978 - WD40 repeat-like
50978 - WD40 repeat-like | 0.05564 | Inherited |
53067,53067
53067 - Actin-like ATPase domain
53067 - Actin-like ATPase domain | 0.07208 | Inherited |
56645,47203
56645 - Acyl-CoA dehydrogenase NM domain-like
47203 - Acyl-CoA dehydrogenase C-terminal domain-like | 0.08052 | Inherited |
55781,109604
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.1339 | Inherited |
57903,47370
57903 - FYVE/PHD zinc finger
47370 - Bromodomain | 0.1339 | Inherited |
55781,55781
55781 - GAF domain-like
55781 - GAF domain-like | 0.1339 | Inherited |
81324,81296
81324 - Voltage-gated potassium channels
81296 - E set domains | 0.1691 | Inherited |
57903,57903
57903 - FYVE/PHD zinc finger
57903 - FYVE/PHD zinc finger | 0.197 | Inherited |
54452,48726
54452 - MHC antigen-recognition domain
48726 - Immunoglobulin | 0.1976 | Inherited |
56436,56436
56436 - C-type lectin-like
56436 - C-type lectin-like | 0.4643 | Inherited |
57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.4951 | Inherited |
(show details)
Supra-domains annotated to this HP term (SPHO level: Least Informative)
Highlighted in gray are those with FDR>0.001
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0 | DIRECT |
69179,69179,69179
69179 - Integrin domains
69179 - Integrin domains
69179 - Integrin domains | 0 | DIRECT |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.04835 | INHERITED FROM: Abnormal urine cytology |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.04835 | INHERITED FROM: Abnormal urine cytology |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.08052 | INHERITED FROM: Renal hypoplasia || Abnormal testis morphology |
52540,52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.08606 | INHERITED FROM: Abnormal male reproductive system physiology || Decreased fertility || Functional abnormality of male internal genitalia || Infertility |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.1182 | INHERITED FROM: Renal insufficiency || Abnormal urine cytology || Decreased urine output || Abnormality of renal excretion || Abnormal urine output || Abnormal renal physiology || Anuria || Hemolytic-uremic syndrome || Acute kidney injury |
55781,55781,109604
55781 - GAF domain-like
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.1339 | INHERITED FROM: Hypogonadism |
49265,49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.4749 | INHERITED FROM: Renal cell carcinoma |
| Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
69318,69179,69179
69318 - Integrin alpha N-terminal domain
69179 - Integrin domains
69179 - Integrin domains | 0 | Direct |
69179,69179,69179
69179 - Integrin domains
69179 - Integrin domains
69179 - Integrin domains | 0 | Direct |
48092,47655,49417
48092 - Transcription factor STAT-4 N-domain
47655 - STAT
49417 - p53-like transcription factors | 0.04835 | Inherited |
47655,49417,55550
47655 - STAT
49417 - p53-like transcription factors
55550 - SH2 domain | 0.04835 | Inherited |
57196,57196,57184
57196 - EGF/Laminin
57196 - EGF/Laminin
57184 - Growth factor receptor domain | 0.08052 | Inherited |
52540,52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.08606 | Inherited |
57535,57535,57535
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain
57535 - Complement control module/SCR domain | 0.1182 | Inherited |
55781,55781,109604
55781 - GAF domain-like
55781 - GAF domain-like
109604 - HD-domain/PDEase-like | 0.1339 | Inherited |
49265,49265,49265
49265 - Fibronectin type III
49265 - Fibronectin type III
49265 - Fibronectin type III | 0.4749 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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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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