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Worm Phenotype (WP): cell cycle variant 
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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: WP Hierarchy (worm phenotype from Wormbase Release WS226)
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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) |
| Smc hinge domain | 0 | DIRECT |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0 | DIRECT |
| Proteasome subunits | 0 | DIRECT |
| LEM domain | 0 | DIRECT |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.000000004692 | DIRECT |
| BTB/POZ domain | 0.00000001676 | DIRECT |
| Skp1 dimerisation domain-like | 0.00000005216 | DIRECT |
| Extended AAA-ATPase domain | 0.0000001427 | DIRECT |
| RecA protein-like (ATPase-domain) | 0.0000006955 | DIRECT |
| Group II chaperonin (CCT, TRIC), apical domain | 0.00006551 | DIRECT |
| Cdc48 domain 2-like | 0.0000975 | DIRECT |
| Anticodon-binding domain | 0.0000975 | DIRECT |
| Cdc48 N-terminal domain-like | 0.0000975 | DIRECT |
| Sm motif of small nuclear ribonucleoproteins, SNRNP | 0.0002339 | DIRECT |
| Single strand DNA-binding domain, SSB | 0.0008287 | DIRECT |
| Motor proteins | 0.001708 | INHERITED FROM: meiosis variant || passage through meiosis defective early emb || X chromosome nondisjunction || meiotic spindle defective |
| F1F0 ATP synthase subunit C | 0.01009 | INHERITED FROM: diakinesis progression during oogenesis variant || chromosome condensation variant || meiosis variant || meiotic progression prophase variant || meiotic chromosome organization variant |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.0125 | INHERITED FROM: cell cycle defective early emb || exaggerated asynchrony early emb || relative cell cycle timing defective early emb || cell cycle timing defective early emb |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.02139 | INHERITED FROM: diakinesis region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| Elongation factors | 0.02654 | INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| Cold shock DNA-binding domain-like | 0.02945 | INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| Translational machinery components | 0.03204 | INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.03647 | INHERITED FROM: diplotene absent during oogenesis || diplotene progression during oogenesis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| L30e/L7ae ribosomal proteins | 0.03647 | INHERITED FROM: diplotene region organization variant || diplotene progression during oogenesis variant || meiosis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| Nucleosome core histones | 0.0628 | INHERITED FROM: diplotene absent during oogenesis || chromosome condensation variant || meiotic chromosome organization variant |
| Nitrogenase iron protein-like | 0.08049 | INHERITED FROM: chromosome condensation variant || diplotene progression during oogenesis variant |
| Clathrin adaptor core protein | 0.1401 | INHERITED FROM: diplotene region organization variant || diplotene progression during oogenesis variant || meiotic progression prophase variant |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.1401 | INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.1586 | INHERITED FROM: pachytene progression during oogenesis variant |
| Cyclin | 0.2201 | INHERITED FROM: cell cycle progression variant |
| Tetratricopeptide repeat (TPR) | 0.383 | INHERITED FROM: meiosis metaphase to anaphase transition block || metaphase to anaphase transition defect |
| Protein serine/threonine phosphatase | 0.4374 | INHERITED FROM: meiosis defective early emb |
| Protein kinases, catalytic subunit | 0.973 | INHERITED FROM: synapsis defective || pachytene arrested germline nuclei |
| SCOP term |
FDR (all) |
Annotation (direct or inherited) |
| Smc hinge domain | 0 | Direct |
| C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Group II chaperonin (CCT, TRIC), intermediate domain | 0 | Direct |
| Proteasome subunits | 0 | Direct |
| LEM domain | 0 | Direct |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
| Group II chaperonin (CCT, TRIC), ATPase domain | 0.000000004692 | Direct |
| BTB/POZ domain | 0.00000001676 | Direct |
| Skp1 dimerisation domain-like | 0.00000005216 | Direct |
| Extended AAA-ATPase domain | 0.0000001427 | Direct |
| RecA protein-like (ATPase-domain) | 0.0000006955 | Direct |
| Group II chaperonin (CCT, TRIC), apical domain | 0.00006551 | Direct |
| Cdc48 domain 2-like | 0.0000975 | Direct |
| Anticodon-binding domain | 0.0000975 | Direct |
| Cdc48 N-terminal domain-like | 0.0000975 | Direct |
| Sm motif of small nuclear ribonucleoproteins, SNRNP | 0.0002339 | Direct |
| Single strand DNA-binding domain, SSB | 0.0008287 | Direct |
| Motor proteins | 0.001708 | Inherited |
| F1F0 ATP synthase subunit C | 0.01009 | Inherited |
| DNA replication initiator (cdc21/cdc54) N-terminal domain | 0.0125 | Inherited |
| Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.02139 | Inherited |
| Elongation factors | 0.02654 | Inherited |
| Cold shock DNA-binding domain-like | 0.02945 | Inherited |
| Translational machinery components | 0.03204 | Inherited |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.03647 | Inherited |
| L30e/L7ae ribosomal proteins | 0.03647 | Inherited |
| Nucleosome core histones | 0.0628 | Inherited |
| Nitrogenase iron protein-like | 0.08049 | Inherited |
| Clathrin adaptor core protein | 0.1401 | Inherited |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.1401 | Inherited |
| Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.1586 | Inherited |
| Cyclin | 0.2201 | Inherited |
| Tetratricopeptide repeat (TPR) | 0.383 | Inherited |
| Protein serine/threonine phosphatase | 0.4374 | Inherited |
| Protein kinases, catalytic subunit | 0.973 | Inherited |
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) |
54585,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | DIRECT |
56091,50249
56091 - DNA ligase/mRNA capping enzyme, catalytic domain
50249 - Nucleic acid-binding proteins | 0 | DIRECT |
50692,54585
50692 - ADC-like
54585 - Cdc48 domain 2-like | 0 | DIRECT |
52540,47917
52540 - P-loop containing nucleoside triphosphate hydrolases
47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | DIRECT |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 0.000000179 | DIRECT |
81333,81333
81333 - F1F0 ATP synthase subunit C
81333 - F1F0 ATP synthase subunit C | 0.00005489 | DIRECT |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.00006965 | DIRECT |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.00006965 | DIRECT |
50249,55681
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases | 0.0002466 | DIRECT |
52374,47323
52374 - Nucleotidylyl transferase
47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.01063 | INHERITED FROM: pachytene progression during oogenesis variant || pachytene region organization variant || meiosis variant || meiotic progression prophase variant |
52540,50447
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins | 0.02743 | INHERITED FROM: pachytene progression during oogenesis variant || pachytene region organization variant || diplotene progression during oogenesis variant || meiosis variant || meiotic progression prophase variant |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.03782 | INHERITED FROM: pachytene progression during oogenesis variant || pachytene region organization variant || diplotene absent during oogenesis || diplotene progression during oogenesis variant || meiotic progression prophase variant |
52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.05912 | INHERITED FROM: meiotic spindle defective early emb || meiotic spindle defective |
48452,48452
48452 - TPR-like
48452 - TPR-like | 0.09281 | INHERITED FROM: metaphase to anaphase transition defect |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.2832 | INHERITED FROM: diplotene progression during oogenesis variant |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.3786 | INHERITED FROM: cell cycle progression variant |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.6242 | INHERITED FROM: diakinesis progression during oogenesis variant |
| Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
54585,52540
54585 - Cdc48 domain 2-like
52540 - P-loop containing nucleoside triphosphate hydrolases | 0 | Direct |
56091,50249
56091 - DNA ligase/mRNA capping enzyme, catalytic domain
50249 - Nucleic acid-binding proteins | 0 | Direct |
50692,54585
50692 - ADC-like
54585 - Cdc48 domain 2-like | 0 | Direct |
52540,47917
52540 - P-loop containing nucleoside triphosphate hydrolases
47917 - C-terminal domain of alpha and beta subunits of F1 ATP synthase | 0 | Direct |
54695,81382
54695 - POZ domain
81382 - Skp1 dimerisation domain-like | 0.000000179 | Direct |
81333,81333
81333 - F1F0 ATP synthase subunit C
81333 - F1F0 ATP synthase subunit C | 0.00005489 | Direct |
48592,54849
48592 - GroEL equatorial domain-like
54849 - GroEL-intermediate domain like | 0.00006965 | Direct |
54849,52029
54849 - GroEL-intermediate domain like
52029 - GroEL apical domain-like | 0.00006965 | Direct |
50249,55681
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases | 0.0002466 | Direct |
52374,47323
52374 - Nucleotidylyl transferase
47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.01063 | Inherited |
52540,50447
52540 - P-loop containing nucleoside triphosphate hydrolases
50447 - Translation proteins | 0.02743 | Inherited |
50447,50465
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0.03782 | Inherited |
52540,52540
52540 - P-loop containing nucleoside triphosphate hydrolases
52540 - P-loop containing nucleoside triphosphate hydrolases | 0.05912 | Inherited |
48452,48452
48452 - TPR-like
48452 - TPR-like | 0.09281 | Inherited |
48371,48371
48371 - ARM repeat
48371 - ARM repeat | 0.2832 | Inherited |
47954,47954
47954 - Cyclin-like
47954 - Cyclin-like | 0.3786 | Inherited |
57196,57196
57196 - EGF/Laminin
57196 - EGF/Laminin | 0.6242 | 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
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 WP 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 WP 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 > cell cycle variant
