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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).
  

Superfamily domains annotated to this WP term (SDWP level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
Ribosomal protein L1	0	DIRECT
The spindle assembly checkpoint protein mad2	0	DIRECT
Histone-fold	0	DIRECT
LEM domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
P-loop containing nucleoside triphosphate hydrolases	0.00003154	DIRECT
Frizzled cysteine-rich domain	0.00003535	DIRECT
Skp1 dimerisation domain-like	0.00004729	DIRECT
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.0001022	DIRECT
ADC-like	0.0003226	DIRECT
Cdc48 domain 2-like	0.0003226	DIRECT
post-AAA+ oligomerization domain-like	0.0003226	DIRECT
Nucleic acid-binding proteins	0.0009007	DIRECT
S15/NS1 RNA-binding domain	0.001373	INHERITED FROM: pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
GroEL-intermediate domain like	0.002051	INHERITED FROM: chromosome condensation variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
GroEL equatorial domain-like	0.002051	INHERITED FROM: chromosome condensation variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Class II aaRS and biotin synthetases	0.00232	INHERITED FROM: pachytene progression during oogenesis variant
CCCH zinc finger	0.002584	INHERITED FROM: cell cleavage variant || division axis defective
"Winged helix" DNA-binding domain	0.003232	INHERITED FROM: spindle orientation defective early emb || mitotic spindle defective early emb || X chromosome nondisjunction
FKBP-like	0.004528	INHERITED FROM: developmental delay || meiosis defective early emb || meiosis variant
Activating enzymes of the ubiquitin-like proteins	0.004757	INHERITED FROM: meiotic chromosome organization variant
Sm-like ribonucleoproteins	0.004954	INHERITED FROM: pachytene region organization variant || pachytene progression during oogenesis variant
GroEL apical domain-like	0.0104	INHERITED FROM: chromosome condensation variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Smc hinge domain	0.01093	INHERITED FROM: anaphase bridging
L30e-like	0.01093	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiosis defective early emb || meiosis variant
ARM repeat	0.01279	INHERITED FROM: cytokinesis variant emb
Actin-like ATPase domain	0.01759	INHERITED FROM: cytokinesis variant emb
POZ domain	0.02573	INHERITED FROM: spindle position variant || univalent meiotic chromosomes || spindle defective early emb || pachytene progression during oogenesis variant || spindle position orientation defective early emb || meiotic chromosome organization variant || mitotic spindle defective early emb || spindle position defective early emb || X chromosome nondisjunction || spindle variant
F1F0 ATP synthase subunit C	0.05613	INHERITED FROM: chromosome condensation variant || mitosis variant || diakinesis progression during oogenesis variant || meiotic chromosome organization variant || meiosis defective early emb || meiotic progression prophase variant || meiosis variant
Translational machinery components	0.05613	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiosis defective early emb || meiotic progression prophase variant || meiosis variant
Ribosomal proteins S24e, L23 and L15e	0.05613	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiosis defective early emb || meiotic progression prophase variant || meiosis variant
DNA repair protein MutS, domain III	0.05613	INHERITED FROM: meiosis defective early emb || meiosis variant
p53-like transcription factors	0.05636	INHERITED FROM: sister cell division timing asynchrony reduced
Ribosomal protein S5 domain 2-like	0.07833	INHERITED FROM: diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
TPR-like	0.09847	INHERITED FROM: meiotic spindle positioning defective || meiosis metaphase to anaphase transition block || mitotic spindle defective early emb || Aba ABp division axis defective early emb
Translation proteins SH3-like domain	0.1118	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Tubulin nucleotide-binding domain-like	0.1118	INHERITED FROM: cytokinesis variant emb || mitosis variant || spindle assembly defective || spindle position orientation defective early emb || mitotic spindle defective early emb || spindle orientation variant || spindle assembly defective early emb || spindle variant
Quinoprotein alcohol dehydrogenase-like	0.1857	INHERITED FROM: developmental delay
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.1857	INHERITED FROM: pachytene region organization variant || pachytene progression during oogenesis variant || meiosis defective early emb || meiosis variant
Tubulin C-terminal domain-like	0.1867	INHERITED FROM: cytokinesis variant emb || mitosis variant || spindle assembly defective || spindle position orientation defective early emb || mitotic spindle defective early emb || spindle orientation variant || spindle assembly defective early emb || spindle variant
EF-hand	0.2342	INHERITED FROM: cell cleavage variant || cell cleavage variant emb
Cyclin-like	0.2538	INHERITED FROM: multiple nuclei early emb || Aba ABp division axis defective early emb || division axis defective
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2998	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || diplotene absent during oogenesis || meiotic progression prophase variant
Prefoldin	0.2998	INHERITED FROM: mitotic spindle defective early emb || spindle variant
Nucleotidylyl transferase	0.4684	INHERITED FROM: pachytene progression during oogenesis variant
Calponin-homology domain, CH-domain	0.5301	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb || cleavage furrow defective || cleavage furrow initiation defective early emb
BAR/IMD domain-like	0.599	INHERITED FROM: cleavage furrow defective early emb || cleavage furrow defective || cleavage furrow initiation defective early emb
SNARE-like	0.641	INHERITED FROM: chromosome condensation variant || diplotene progression during oogenesis variant
Translation proteins	0.6499	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Protein kinase-like (PK-like)	0.6521	INHERITED FROM: pachytene arrested germline nuclei || synapsis defective
PDZ domain-like	0.6563	INHERITED FROM: cell division polarity variant
GTPase activation domain, GAP	0.6908	INHERITED FROM: cleavage furrow defective early emb || cleavage furrow defective
Homeodomain-like	0.7469	INHERITED FROM: sister cell division timing asynchrony reduced

Family domains annotated to this WP term (SDWP level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Profilin (actin-binding protein)	0	DIRECT
Ribosomal protein L1	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
N-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
Nucleosome core histones	0	DIRECT
DNA gyrase/MutL, second domain	0	DIRECT
LEM domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0.0000001352	DIRECT
Extended AAA-ATPase domain	0.0000009111	DIRECT
RecA protein-like (ATPase-domain)	0.000008505	DIRECT
Skp1 dimerisation domain-like	0.00004235	DIRECT
Frizzled cysteine-rich domain	0.00006647	DIRECT
BTB/POZ domain	0.00007451	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0.0005093	DIRECT
Cdc48 N-terminal domain-like	0.0005093	DIRECT
Cdc48 domain 2-like	0.0005093	DIRECT
Anticodon-binding domain	0.0005093	DIRECT
Anticodon-binding domain of Class II aaRS	0.0005093	DIRECT
DNA gyrase/MutL, N-terminal domain	0.0005093	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0.001745	INHERITED FROM: chromosome condensation variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.002017	INHERITED FROM: pachytene progression during oogenesis variant
DEP domain	0.002155	INHERITED FROM: spindle defective early emb || mitotic spindle defective early emb || spindle variant
Actin/HSP70	0.003618	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb
Sm motif of small nuclear ribonucleoproteins, SNRNP	0.004084	INHERITED FROM: chromosome condensation variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Armadillo repeat	0.004326	INHERITED FROM: spindle orientation defective early emb || spindle defective early emb || mitotic spindle defective early emb || spindle variant
CCCH zinc finger	0.007213	INHERITED FROM: cell cleavage variant || division axis defective
FKBP immunophilin/proline isomerase	0.008041	INHERITED FROM: developmental delay || meiosis defective early emb
Motor proteins	0.00945	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb || meiotic spindle defective || spindle defective early emb || cleavage furrow defective || meiosis defective early emb || X chromosome nondisjunction || meiosis variant || spindle variant
DNA replication initiator (cdc21/cdc54) N-terminal domain	0.009464	INHERITED FROM: cytokinesis variant emb || cytokinesis defective early emb || sister chromatid segregation defective early emb || multiple nuclei early emb || cytokinesis variant
Smc hinge domain	0.02183	INHERITED FROM: anaphase bridging
L30e/L7ae ribosomal proteins	0.02183	INHERITED FROM: diplotene region organization variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiosis defective early emb || meiosis variant
G proteins	0.03652	INHERITED FROM: cytokinesis variant emb || spindle position orientation defective early emb || mitotic spindle defective early emb
Translational machinery components	0.03897	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
F1F0 ATP synthase subunit C	0.04995	INHERITED FROM: chromosome condensation variant || mitosis variant || diakinesis progression during oogenesis variant || meiotic chromosome organization variant || meiosis defective early emb || meiotic progression prophase variant || meiosis variant
DNA repair protein MutS, domain III	0.04995	INHERITED FROM: meiosis defective early emb || meiosis variant
Pumilio repeat	0.09407	INHERITED FROM: cytokinesis variant emb || cytokinesis failure || multiple nuclei early emb || cytokinesis fails early emb
Tubulin, GTPase domain	0.1036	INHERITED FROM: cytokinesis variant emb || mitosis variant || spindle defective early emb || spindle assembly defective || spindle position orientation defective early emb || mitotic spindle defective early emb || spindle orientation variant || spindle assembly defective early emb || spindle variant
Cold shock DNA-binding domain-like	0.112	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Prefoldin	0.1512	INHERITED FROM: mitotic spindle defective early emb || spindle variant
ABC transporter ATPase domain-like	0.1555	INHERITED FROM: anaphase bridging
Tubulin, C-terminal domain	0.176	INHERITED FROM: cytokinesis variant emb || mitosis variant || spindle assembly defective || spindle position orientation defective early emb || mitotic spindle defective early emb || spindle orientation variant || spindle assembly defective early emb || spindle variant
Cyclin	0.2626	INHERITED FROM: multiple nuclei early emb || Aba ABp division axis defective early emb || division axis defective
Elongation factors	0.2717	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.2795	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || meiosis defective early emb
Nitrogenase iron protein-like	0.2841	INHERITED FROM: chromosome condensation variant || mitosis variant || diplotene progression during oogenesis variant
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2841	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant || diplotene absent during oogenesis || meiotic progression prophase variant
Clathrin adaptor core protein	0.4264	INHERITED FROM: diplotene region organization variant || diplotene progression during oogenesis variant || meiotic progression prophase variant
Protein kinases, catalytic subunit	0.4371	INHERITED FROM: pachytene arrested germline nuclei || synapsis defective
Class I aminoacyl-tRNA synthetases (RS), catalytic domain	0.4853	INHERITED FROM: pachytene progression during oogenesis variant
Tetratricopeptide repeat (TPR)	0.4907	INHERITED FROM: meiosis metaphase to anaphase transition block
BCR-homology GTPase activation domain (BH-domain)	0.5202	INHERITED FROM: cleavage furrow defective early emb || cleavage furrow defective
Calponin-homology domain, CH-domain	0.5204	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb || cleavage furrow defective || cleavage furrow initiation defective early emb
PDZ domain	0.5536	INHERITED FROM: spindle defective early emb || cell division polarity variant || mitotic spindle defective early emb || spindle variant
Homeodomain	0.6914	INHERITED FROM: sister cell division timing asynchrony reduced

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.

Supra-domains annotated to this WP term (SPWP level: Moderately Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Ribosomal protein L1	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
LEM domain	0	DIRECT
Histone-fold	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
The spindle assembly checkpoint protein mad2	0	DIRECT
P-loop containing nucleoside triphosphate hydrolases	0.00002559	DIRECT
Frizzled cysteine-rich domain	0.0000287	DIRECT
Skp1 dimerisation domain-like	0.00003844	DIRECT
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.00008331	DIRECT
Cdc48 domain 2-like	0.0002644	DIRECT
ADC-like	0.0002644	DIRECT
post-AAA+ oligomerization domain-like	0.0002644	DIRECT
Nucleic acid-binding proteins	0.0007444	DIRECT
S15/NS1 RNA-binding domain	0.00114	INHERITED FROM: meiotic progression prophase variant || pachytene region organization variant || pachytene progression during oogenesis variant
GroEL equatorial domain-like	0.001709	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
GroEL-intermediate domain like	0.001709	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
Class II aaRS and biotin synthetases	0.00194	INHERITED FROM: diakinesis region organization variant || pachytene progression during oogenesis variant
CCCH zinc finger	0.002163	INHERITED FROM: division axis defective || cell cleavage variant
"Winged helix" DNA-binding domain	0.002716	INHERITED FROM: mitotic spindle defective early emb || X chromosome nondisjunction || spindle orientation defective early emb
FKBP-like	0.00382	INHERITED FROM: meiosis variant || meiosis defective early emb || developmental delay
Activating enzymes of the ubiquitin-like proteins	0.004015	INHERITED FROM: meiotic chromosome organization variant
Sm-like ribonucleoproteins	0.004184	INHERITED FROM: pachytene region organization variant || pachytene progression during oogenesis variant
GroEL apical domain-like	0.008884	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
Smc hinge domain	0.009347	INHERITED FROM: anaphase bridging
L30e-like	0.009347	INHERITED FROM: meiosis variant || meiosis defective early emb || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
ARM repeat	0.01097	INHERITED FROM: cytokinesis variant emb
Actin-like ATPase domain	0.01516	INHERITED FROM: cytokinesis variant emb
POZ domain	0.02239	INHERITED FROM: spindle position variant || meiotic chromosome organization variant || spindle position defective early emb || spindle defective early emb || mitotic spindle defective early emb || spindle variant || spindle position orientation defective early emb || univalent meiotic chromosomes || pachytene progression during oogenesis variant || X chromosome nondisjunction
DNA repair protein MutS, domain III	0.04972	INHERITED FROM: meiosis variant || meiosis defective early emb
Translational machinery components	0.04972	INHERITED FROM: meiotic progression prophase variant || meiosis variant || meiosis defective early emb || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
Ribosomal proteins S24e, L23 and L15e	0.04972	INHERITED FROM: meiotic progression prophase variant || meiosis variant || meiosis defective early emb || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
F1F0 ATP synthase subunit C	0.04972	INHERITED FROM: diakinesis progression during oogenesis variant || meiotic progression prophase variant || meiotic chromosome organization variant || meiosis variant || meiosis defective early emb || chromosome condensation variant || mitosis variant
p53-like transcription factors	0.04993	INHERITED FROM: sister cell division timing asynchrony reduced
Ribosomal protein S5 domain 2-like	0.06999	INHERITED FROM: diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
TPR-like	0.08865	INHERITED FROM: meiosis metaphase to anaphase transition block || Aba ABp division axis defective early emb || mitotic spindle defective early emb || meiotic spindle positioning defective
Tubulin nucleotide-binding domain-like	0.101	INHERITED FROM: spindle assembly defective early emb || spindle orientation variant || spindle defective early emb || mitotic spindle defective early emb || spindle variant || spindle position orientation defective early emb || cytokinesis variant emb || spindle assembly defective || mitosis variant
Translation proteins SH3-like domain	0.101	INHERITED FROM: meiotic progression prophase variant || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
Quinoprotein alcohol dehydrogenase-like	0.1702	INHERITED FROM: developmental delay
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.1702	INHERITED FROM: meiosis variant || meiosis defective early emb || pachytene region organization variant || pachytene progression during oogenesis variant
Tubulin C-terminal domain-like	0.1711	INHERITED FROM: spindle assembly defective early emb || spindle orientation variant || mitotic spindle defective early emb || spindle variant || spindle position orientation defective early emb || cytokinesis variant emb || spindle assembly defective || mitosis variant
EF-hand	0.2166	INHERITED FROM: cell cleavage variant emb || cell cleavage variant
Cyclin-like	0.2354	INHERITED FROM: Aba ABp division axis defective early emb || division axis defective || multiple nuclei early emb
Prefoldin	0.2803	INHERITED FROM: mitotic spindle defective early emb || spindle variant
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2803	INHERITED FROM: meiotic progression prophase variant || diplotene absent during oogenesis || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
Nucleotidylyl transferase	0.4465	INHERITED FROM: pachytene progression during oogenesis variant
Calponin-homology domain, CH-domain	0.5075	INHERITED FROM: cleavage furrow defective || cytokinesis variant emb || cleavage furrow defective early emb || cleavage furrow initiation defective early emb
BAR/IMD domain-like	0.5767	INHERITED FROM: cleavage furrow defective || cleavage furrow defective early emb || cleavage furrow initiation defective early emb
SNARE-like	0.6189	INHERITED FROM: diplotene progression during oogenesis variant || chromosome condensation variant
Translation proteins	0.6279	INHERITED FROM: meiotic progression prophase variant || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
Protein kinase-like (PK-like)	0.6301	INHERITED FROM: pachytene arrested germline nuclei || synapsis defective
PDZ domain-like	0.6344	INHERITED FROM: cell division polarity variant
GTPase activation domain, GAP	0.6696	INHERITED FROM: cleavage furrow defective || cleavage furrow defective early emb
Homeodomain-like	0.7274	INHERITED FROM: sister cell division timing asynchrony reduced

Supra-domains annotated to this WP term (SPWP level: Moderately 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)
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
55874,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 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
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54695,81382 54695 - POZ domain 81382 - Skp1 dimerisation domain-like	0.00008331	DIRECT
81333,81333 81333 - F1F0 ATP synthase subunit C 81333 - F1F0 ATP synthase subunit C	0.0002644	DIRECT
55681,52954 55681 - Class II aaRS and biotin synthetases 52954 - Class II aaRS ABD-related	0.0002644	DIRECT
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0.0002644	DIRECT
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0.00114	INHERITED FROM: meiotic progression prophase variant || meiosis variant || meiosis defective early emb || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant || diplotene region organization variant
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0.00114	INHERITED FROM: meiosis variant || meiosis defective early emb || developmental delay
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.001709	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.001709	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	0.001931	INHERITED FROM: division axis defective || cell cleavage variant
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.007631	INHERITED FROM: cytokinesis variant emb
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.02166	INHERITED FROM: meiosis variant || meiosis defective early emb || pachytene region organization variant || pachytene progression during oogenesis variant
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.03679	INHERITED FROM: mitotic spindle defective early emb || diplotene progression during oogenesis variant
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0.04972	INHERITED FROM: meiosis variant || meiosis defective early emb
48452,48452 48452 - TPR-like 48452 - TPR-like	0.06345	INHERITED FROM: mitotic spindle defective early emb
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.101	INHERITED FROM: Aba ABp division axis defective early emb || division axis defective || multiple nuclei early emb
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0.101	INHERITED FROM: spindle assembly defective early emb || spindle orientation variant || spindle defective early emb || mitotic spindle defective early emb || spindle variant || spindle position orientation defective early emb || cytokinesis variant emb || spindle assembly defective || mitosis variant
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	0.2658	INHERITED FROM: meiotic progression prophase variant || meiosis defective early emb || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2803	INHERITED FROM: meiotic progression prophase variant || diplotene absent during oogenesis || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.2822	INHERITED FROM: meiotic spindle defective || meiotic spindle defective early emb
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.9964	INHERITED FROM: diakinesis progression during oogenesis variant

Supra-domains annotated to this WP term (SPWP level: Moderately 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)
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.001709	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2803	INHERITED FROM: meiotic progression prophase variant || diplotene absent during oogenesis || pachytene region organization variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant

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.