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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)
Profilin (actin-binding protein)	0	DIRECT
LEM domain	0	DIRECT
The spindle assembly checkpoint protein mad2	0	DIRECT
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
Smc hinge domain	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
Histone-fold	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0.000001918	DIRECT
P-loop containing nucleoside triphosphate hydrolases	0.000003846	DIRECT
Skp1 dimerisation domain-like	0.000008989	DIRECT
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.00002159	DIRECT
Frizzled cysteine-rich domain	0.00002669	DIRECT
Nucleic acid-binding proteins	0.0002128	DIRECT
ADC-like	0.0002575	DIRECT
post-AAA+ oligomerization domain-like	0.0002575	DIRECT
Cdc48 domain 2-like	0.0002575	DIRECT
GroEL equatorial domain-like	0.0009018	DIRECT
GroEL-intermediate domain like	0.0009018	DIRECT
S15/NS1 RNA-binding domain	0.001109	INHERITED FROM: meiotic progression prophase variant || pachytene region organization variant || pachytene progression during oogenesis variant
CCCH zinc finger	0.001779	INHERITED FROM: cell cleavage variant || division axis defective
Sm-like ribonucleoproteins	0.002104	INHERITED FROM: pachytene region organization variant || pachytene progression during oogenesis variant
"Winged helix" DNA-binding domain	0.003086	INHERITED FROM: mitotic spindle defective early emb || X chromosome nondisjunction
ARM repeat	0.00406	INHERITED FROM: cytokinesis variant emb
GroEL apical domain-like	0.004926	INHERITED FROM: meiotic progression prophase variant || chromosome condensation variant || pachytene progression during oogenesis variant
POZ domain	0.006491	INHERITED FROM: spindle position defective early emb || mitotic spindle defective early emb || spindle variant || X chromosome nondisjunction || univalent meiotic chromosomes || spindle position variant || spindle position orientation defective early emb || meiosis variant || pachytene progression during oogenesis variant || spindle defective early emb
Actin-like ATPase domain	0.03411	INHERITED FROM: cytokinesis variant emb
Class II aaRS and biotin synthetases	0.03483	INHERITED FROM: meiotic progression prophase variant || diakinesis region organization variant || pachytene progression during oogenesis variant
Ribosomal proteins S24e, L23 and L15e	0.03789	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis variant || pachytene progression during oogenesis variant || meiosis defective early emb
p53-like transcription factors	0.066	INHERITED FROM: sister cell division timing asynchrony reduced
Tubulin nucleotide-binding domain-like	0.066	INHERITED FROM: spindle orientation variant || mitotic spindle defective early emb || cytokinesis variant emb || spindle assembly defective || spindle position orientation defective early emb || mitosis variant
Translation proteins SH3-like domain	0.066	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant
Cyclin-like	0.1036	INHERITED FROM: Aba ABp division axis defective early emb || multiple nuclei early emb || division axis defective
Tubulin C-terminal domain-like	0.1161	INHERITED FROM: spindle orientation variant || mitotic spindle defective early emb || cytokinesis variant emb || spindle assembly defective || spindle position orientation defective early emb || mitosis variant
F1F0 ATP synthase subunit C	0.1166	INHERITED FROM: diakinesis progression during oogenesis variant || meiotic progression prophase variant || chromosome condensation variant || meiotic chromosome organization variant || meiosis variant || mitosis variant || meiosis defective early emb
Translational machinery components	0.1166	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis variant || pachytene progression during oogenesis variant || meiosis defective early emb
L30e-like	0.1222	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis variant || pachytene progression during oogenesis variant || meiosis defective early emb
Ribosomal protein S5 domain 2-like	0.1408	INHERITED FROM: diplotene progression during oogenesis variant || pachytene progression during oogenesis variant
TPR-like	0.1923	INHERITED FROM: mitotic spindle defective early emb || spindle variant || Aba ABp division axis defective early emb || meiotic spindle positioning defective || meiosis metaphase to anaphase transition block
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.2108	INHERITED FROM: meiotic progression prophase variant || pachytene region organization variant || meiosis variant || pachytene progression during oogenesis variant || meiosis defective early emb
Prefoldin	0.2253	INHERITED FROM: mitotic spindle defective early emb || spindle variant
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2253	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || diplotene absent during oogenesis || pachytene region organization variant || pachytene progression during oogenesis variant
BAR/IMD domain-like	0.255	INHERITED FROM: cleavage furrow defective early emb || cleavage furrow initiation defective early emb || cleavage furrow defective
Calponin-homology domain, CH-domain	0.3813	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb || cleavage furrow initiation defective early emb || cleavage furrow defective
Nucleotidylyl transferase	0.4648	INHERITED FROM: pachytene progression during oogenesis variant
Translation proteins	0.5016	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant
SNARE-like	0.5152	INHERITED FROM: diplotene progression during oogenesis variant || chromosome condensation variant
GTPase activation domain, GAP	0.5542	INHERITED FROM: cleavage furrow defective early emb || cleavage furrow defective
Homeodomain-like	0.7564	INHERITED FROM: sister cell division timing asynchrony reduced
PDZ domain-like	0.7851	INHERITED FROM: cell division polarity variant
PX domain	0.8343	INHERITED FROM: cell division polarity variant
Protein kinase-like (PK-like)	0.8792	INHERITED FROM: synapsis defective || pachytene arrested germline nuclei

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)
N-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
C-terminal domain of alpha and beta subunits of F1 ATP synthase	0	DIRECT
Proteasome subunits	0	DIRECT
Nucleosome core histones	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
LEM domain	0	DIRECT
Smc hinge domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
Group II chaperonin (CCT, TRIC), ATPase domain	0.00000008045	DIRECT
Extended AAA-ATPase domain	0.00000009305	DIRECT
RecA protein-like (ATPase-domain)	0.000005737	DIRECT
Skp1 dimerisation domain-like	0.000008379	DIRECT
BTB/POZ domain	0.00001029	DIRECT
Frizzled cysteine-rich domain	0.00004768	DIRECT
Ubiquitin activating enzymes (UBA)	0.00004768	DIRECT
Cdc48 N-terminal domain-like	0.0003893	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0.0003893	DIRECT
Cdc48 domain 2-like	0.0003893	DIRECT
Anticodon-binding domain	0.0003893	DIRECT
Anticodon-binding domain of Class II aaRS	0.0003893	DIRECT
Group II chaperonin (CCT, TRIC), apical domain	0.0007741	DIRECT
DEP domain	0.001668	INHERITED FROM: mitotic spindle defective early emb || spindle variant || spindle defective early emb
Armadillo repeat	0.001841	INHERITED FROM: mitotic spindle defective early emb || spindle variant || spindle orientation defective early emb
Sm motif of small nuclear ribonucleoproteins, SNRNP	0.002006	INHERITED FROM: meiotic progression prophase variant || chromosome condensation variant || pachytene region organization variant || pachytene progression during oogenesis variant
Motor proteins	0.002986	INHERITED FROM: spindle variant || X chromosome nondisjunction || cleavage furrow defective early emb || cytokinesis variant emb || meiosis variant || meiotic spindle defective || cleavage furrow defective || meiosis defective early emb || spindle defective early emb
CCCH zinc finger	0.004709	INHERITED FROM: cell cleavage variant || division axis defective
DNA replication initiator (cdc21/cdc54) N-terminal domain	0.00517	INHERITED FROM: sister chromatid segregation defective early emb || multiple nuclei early emb || cytokinesis variant emb || cytokinesis defective early emb || cytokinesis variant
Actin/HSP70	0.01051	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb
G proteins	0.01295	INHERITED FROM: mitotic spindle defective early emb || cytokinesis variant emb || spindle position orientation defective early emb
Translational machinery components	0.02262	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.03188	INHERITED FROM: meiotic progression prophase variant || diakinesis region organization variant || pachytene progression during oogenesis variant
Pumilio repeat	0.05786	INHERITED FROM: cytokinesis failure || multiple nuclei early emb || cytokinesis variant emb || cytokinesis fails early emb
Cold shock DNA-binding domain-like	0.06056	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant
Tubulin, GTPase domain	0.06103	INHERITED FROM: spindle orientation variant || mitotic spindle defective early emb || cytokinesis variant emb || spindle assembly defective || spindle position orientation defective early emb || spindle assembly defective early emb || mitosis variant
L30e/L7ae ribosomal proteins	0.1067	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || diplotene region organization variant || pachytene region organization variant || meiosis variant || pachytene progression during oogenesis variant || meiosis defective early emb
Prefoldin	0.1067	INHERITED FROM: mitotic spindle defective early emb || spindle variant
F1F0 ATP synthase subunit C	0.1067	INHERITED FROM: diakinesis progression during oogenesis variant || meiotic progression prophase variant || chromosome condensation variant || meiotic chromosome organization variant || meiosis variant || mitosis variant || meiosis defective early emb
Cyclin	0.1085	INHERITED FROM: Aba ABp division axis defective early emb || multiple nuclei early emb || division axis defective
Tubulin, C-terminal domain	0.1085	INHERITED FROM: spindle orientation variant || mitotic spindle defective early emb || cytokinesis variant emb || spindle assembly defective || spindle position orientation defective early emb || spindle assembly defective early emb || mitosis variant
ABC transporter ATPase domain-like	0.1561	INHERITED FROM: anaphase bridging
Elongation factors	0.1844	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant
Nitrogenase iron protein-like	0.2113	INHERITED FROM: diplotene progression during oogenesis variant || chromosome condensation variant || mitosis variant
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2113	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || diplotene absent during oogenesis || pachytene region organization variant || pachytene progression during oogenesis variant
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.3311	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant || pachytene progression during oogenesis variant
Clathrin adaptor core protein	0.3311	INHERITED FROM: meiotic progression prophase variant || diplotene progression during oogenesis variant || diplotene region organization variant
Calponin-homology domain, CH-domain	0.3729	INHERITED FROM: cleavage furrow defective early emb || cytokinesis variant emb || cleavage furrow initiation defective early emb || cleavage furrow defective
BCR-homology GTPase activation domain (BH-domain)	0.4019	INHERITED FROM: cleavage furrow defective early emb || cleavage furrow defective
Class I aminoacyl-tRNA synthetases (RS), catalytic domain	0.5045	INHERITED FROM: pachytene progression during oogenesis variant
Tetratricopeptide repeat (TPR)	0.5972	INHERITED FROM: meiosis metaphase to anaphase transition block
PDZ domain	0.6268	INHERITED FROM: cell division polarity variant || mitotic spindle defective early emb || spindle variant || spindle defective early emb
Homeodomain	0.7213	INHERITED FROM: sister cell division timing asynchrony reduced
Protein kinases, catalytic subunit	0.7468	INHERITED FROM: synapsis defective || pachytene arrested germline nuclei
PX domain	0.8251	INHERITED FROM: cell division polarity variant

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)
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
Histone-fold	0	DIRECT
Smc hinge domain	0	DIRECT
Profilin (actin-binding protein)	0	DIRECT
The spindle assembly checkpoint protein mad2	0	DIRECT
LEM domain	0	DIRECT
Activating enzymes of the ubiquitin-like proteins	0.00000156	DIRECT
P-loop containing nucleoside triphosphate hydrolases	0.000003133	DIRECT
Skp1 dimerisation domain-like	0.00000733	DIRECT
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.00001766	DIRECT
Frizzled cysteine-rich domain	0.00002184	DIRECT
Nucleic acid-binding proteins	0.0001755	DIRECT
Cdc48 domain 2-like	0.0002126	DIRECT
ADC-like	0.0002126	DIRECT
post-AAA+ oligomerization domain-like	0.0002126	DIRECT
GroEL equatorial domain-like	0.0007518	DIRECT
GroEL-intermediate domain like	0.0007518	DIRECT
S15/NS1 RNA-binding domain	0.0009261	DIRECT
CCCH zinc finger	0.001492	INHERITED FROM: cell cleavage variant || division axis defective
Sm-like ribonucleoproteins	0.00177	INHERITED FROM: pachytene progression during oogenesis variant || pachytene region organization variant
"Winged helix" DNA-binding domain	0.002609	INHERITED FROM: mitotic spindle defective early emb || spindle rotation variant || X chromosome nondisjunction
ARM repeat	0.003442	INHERITED FROM: cytokinesis variant emb
GroEL apical domain-like	0.004188	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || chromosome condensation variant
POZ domain	0.005544	INHERITED FROM: meiosis variant || pachytene progression during oogenesis variant || mitotic spindle defective early emb || spindle position defective early emb || spindle defective early emb || spindle position variant || spindle variant || X chromosome nondisjunction || univalent meiotic chromosomes || spindle position orientation defective early emb
Actin-like ATPase domain	0.03004	INHERITED FROM: cytokinesis variant emb
Class II aaRS and biotin synthetases	0.03068	INHERITED FROM: meiotic progression prophase variant || diakinesis region organization variant || pachytene progression during oogenesis variant
Ribosomal proteins S24e, L23 and L15e	0.03345	INHERITED FROM: meiotic progression prophase variant || meiosis variant || pachytene progression during oogenesis variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis defective early emb
Translation proteins SH3-like domain	0.05895	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || diplotene progression during oogenesis variant || pachytene region organization variant
p53-like transcription factors	0.05895	INHERITED FROM: sister cell division timing asynchrony reduced
Tubulin nucleotide-binding domain-like	0.05895	INHERITED FROM: spindle assembly defective early emb || spindle orientation variant || mitotic spindle defective early emb || mitosis variant || cytokinesis variant emb || spindle position orientation defective early emb || spindle assembly defective
Cyclin-like	0.09368	INHERITED FROM: multiple nuclei early emb || division axis defective || Aba ABp division axis defective early emb
Tubulin C-terminal domain-like	0.1053	INHERITED FROM: spindle assembly defective early emb || spindle orientation variant || mitotic spindle defective early emb || mitosis variant || cytokinesis variant emb || spindle position orientation defective early emb || spindle assembly defective
F1F0 ATP synthase subunit C	0.1058	INHERITED FROM: meiotic progression prophase variant || diakinesis progression during oogenesis variant || meiosis variant || chromosome condensation variant || meiotic chromosome organization variant || mitosis variant || meiosis defective early emb
Translational machinery components	0.1058	INHERITED FROM: meiotic progression prophase variant || meiosis variant || pachytene progression during oogenesis variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis defective early emb
L30e-like	0.1109	INHERITED FROM: meiotic progression prophase variant || meiosis variant || pachytene progression during oogenesis variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis defective early emb
Ribosomal protein S5 domain 2-like	0.1283	INHERITED FROM: pachytene progression during oogenesis variant || diplotene progression during oogenesis variant
TPR-like	0.177	INHERITED FROM: mitotic spindle defective early emb || spindle variant || meiotic spindle positioning defective || meiosis metaphase to anaphase transition block || Aba ABp division axis defective early emb
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.1946	INHERITED FROM: meiotic progression prophase variant || meiosis variant || pachytene progression during oogenesis variant || pachytene region organization variant || meiosis defective early emb
Prefoldin	0.2085	INHERITED FROM: mitotic spindle defective early emb || spindle variant
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2085	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || diplotene absent during oogenesis || diplotene progression during oogenesis variant || pachytene region organization variant
BAR/IMD domain-like	0.2372	INHERITED FROM: cleavage furrow initiation defective early emb || cleavage furrow defective || cleavage furrow defective early emb
Calponin-homology domain, CH-domain	0.3608	INHERITED FROM: cleavage furrow initiation defective early emb || cytokinesis variant emb || cleavage furrow defective || cleavage furrow defective early emb
Nucleotidylyl transferase	0.4437	INHERITED FROM: pachytene progression during oogenesis variant
Translation proteins	0.4802	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || diplotene progression during oogenesis variant || pachytene region organization variant
SNARE-like	0.4936	INHERITED FROM: chromosome condensation variant || diplotene progression during oogenesis variant
GTPase activation domain, GAP	0.5326	INHERITED FROM: cleavage furrow defective || cleavage furrow defective early emb
Homeodomain-like	0.737	INHERITED FROM: sister cell division timing asynchrony reduced
PDZ domain-like	0.7661	INHERITED FROM: cell division polarity variant
PX domain	0.8167	INHERITED FROM: cell division polarity variant
Protein kinase-like (PK-like)	0.8634	INHERITED FROM: pachytene arrested germline nuclei || synapsis defective

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
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	0.00001766	DIRECT
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0.0002126	DIRECT
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.0007518	DIRECT
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.0007518	DIRECT
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases	0.0009261	DIRECT
90229,90229 90229 - CCCH zinc finger 90229 - CCCH zinc finger	0.001414	INHERITED FROM: cell cleavage variant || division axis defective
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.01779	INHERITED FROM: cytokinesis variant emb
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.03242	INHERITED FROM: mitotic spindle defective early emb || diplotene progression during oogenesis variant
52374,47323 52374 - Nucleotidylyl transferase 47323 - Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.03345	INHERITED FROM: meiotic progression prophase variant || meiosis variant || pachytene progression during oogenesis variant || pachytene region organization variant || meiosis defective early emb
81333,81333 81333 - F1F0 ATP synthase subunit C 81333 - F1F0 ATP synthase subunit C	0.03345	INHERITED FROM: meiotic progression prophase variant || diakinesis progression during oogenesis variant || meiosis variant || chromosome condensation variant || meiotic chromosome organization variant || mitosis variant || meiosis defective early emb
48452,48452 48452 - TPR-like 48452 - TPR-like	0.05776	INHERITED FROM: mitotic spindle defective early emb
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0.05895	INHERITED FROM: spindle assembly defective early emb || spindle orientation variant || mitotic spindle defective early emb || mitosis variant || cytokinesis variant emb || spindle position orientation defective early emb || spindle assembly defective
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.05895	INHERITED FROM: multiple nuclei early emb || division axis defective || Aba ABp division axis defective early emb
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	0.1799	INHERITED FROM: meiotic progression prophase variant || meiosis variant || pachytene progression during oogenesis variant || diplotene progression during oogenesis variant || pachytene region organization variant || meiosis defective early emb
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2085	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || diplotene absent during oogenesis || diplotene progression during oogenesis variant || pachytene region organization variant
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.3618	INHERITED FROM: meiotic spindle defective || meiotic spindle defective early emb
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.9505	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	0.0007518	DIRECT
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0.2085	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || diplotene absent during oogenesis || diplotene progression during oogenesis variant || pachytene region organization 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.