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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 XA term (SDXA level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
Synuclein	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
PriA/YqbF domain	0	DIRECT
14-3-3 protein	0	DIRECT
Homeodomain-like	0	DIRECT
SRF-like	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
PLP-binding barrel	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
"Winged helix" DNA-binding domain	0.000000000000001469	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.000000000000005868	DIRECT
RNA-binding domain, RBD	0.000000000164	DIRECT
Cytokine	0.0000001431	DIRECT
Frizzled cysteine-rich domain	0.0000003987	DIRECT
HMG-box	0.00005027	DIRECT
Cystine-knot cytokines	0.0002243	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0003207	DIRECT
Sema domain	0.0003711	DIRECT
SAP domain	0.0007792	DIRECT
p53-like transcription factors	0.001589	INHERITED FROM: lung bud || foregut || lung primordium || involuted ventral mesoderm || neurogenic placode || lower blastopore lip || cranial placode
Snake toxin-like	0.001706	INHERITED FROM: anterior dorsal lateral plate region || ventral mesoderm || lateral plate mesoderm || dorsal lateral plate mesoderm || involuted dorsal mesoderm
Orange domain-like	0.002718	INHERITED FROM: neurogenic placode || paraxial mesoderm || cranial placode
Plexin repeat	0.007295	INHERITED FROM: otic placode || presumptive midbrain-hindbrain boundary || cranial placode || involuted dorsal mesoderm
lambda repressor-like DNA-binding domains	0.01573	INHERITED FROM: neurogenic placode || presumptive midbrain-hindbrain boundary || cranial placode
GroEL-intermediate domain like	0.02125	INHERITED FROM: anterior dorsal lateral plate region
GroEL equatorial domain-like	0.02125	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.04584	INHERITED FROM: anterior dorsal lateral plate region
beta-beta-alpha zinc fingers	0.09994	INHERITED FROM: lateral plate mesoderm || splanchnic layer of lateral plate mesoderm || presumptive rhombomere
Mannose 6-phosphate receptor domain	0.171	INHERITED FROM: cement gland primordium
Transducin (alpha subunit), insertion domain	0.1837	INHERITED FROM: dorsal marginal zone
Alpha-macroglobulin receptor domain	0.1952	INHERITED FROM: foregut || midgut || hindgut
TIMP-like	0.2122	INHERITED FROM: foregut || stomodeal-hypophyseal primordium || anterior neural tube || prechordal plate
Globin-like	0.2164	INHERITED FROM: anterior dorsal lateral plate region || lateral plate mesoderm
EGF/Laminin	0.2237	INHERITED FROM: axial mesoderm
Kazal-type serine protease inhibitors	0.2336	INHERITED FROM: axial mesoderm
FnI-like domain	0.2649	INHERITED FROM: axial mesoderm || prechordal plate || neural tube
Tropomyosin	0.2649	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.3413	INHERITED FROM: eye primordium
Protein kinase-like (PK-like)	0.4721	INHERITED FROM: lateral plate mesoderm
Terpenoid cyclases/Protein prenyltransferases	0.5217	INHERITED FROM: midgut || hindgut
LDL receptor-like module	0.639	INHERITED FROM: hindgut
Nuclear receptor ligand-binding domain	0.6514	INHERITED FROM: foregut
E set domains	0.9214	INHERITED FROM: liver primordium

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

SCOP term	FDR (all)	Annotation (direct or inherited)
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
Eukaryotic ODC-like	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
Noggin	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	DIRECT
Homeodomain	0	DIRECT
Synuclein	0	DIRECT
SRF-like	0	DIRECT
Pointed domain	0	DIRECT
Ran-binding domain	0	DIRECT
Hedgehog (development protein), N-terminal signaling domain	0	DIRECT
14-3-3 protein	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
SH3BGR (SH3-binding, glutamic acid-rich protein-like)	0	DIRECT
Guanido kinase catalytic domain	0	DIRECT
Alanine racemase-like, N-terminal domain	0	DIRECT
Troponin I	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.00000000000002875	DIRECT
Forkhead DNA-binding domain	0.0000000000001642	DIRECT
Canonical RBD	0.00000000002451	DIRECT
ets domain	0.000000019	DIRECT
Transforming growth factor (TGF)-beta	0.0000004286	DIRECT
Frizzled cysteine-rich domain	0.0000005521	DIRECT
HMG-box	0.00007971	DIRECT
Sema domain	0.0001816	DIRECT
T-box	0.0002266	DIRECT
POU-specific domain	0.0005924	DIRECT
SAP domain	0.0008976	DIRECT
Cyclin	0.0009098	DIRECT
LIM domain	0.00169	INHERITED FROM: cranial placode
Hairy Orange domain	0.002769	INHERITED FROM: neurogenic placode || paraxial mesoderm || cranial placode
P4 origin-binding domain-like	0.004062	INHERITED FROM: optic vesicle || neurogenic placode || otic placode || cranial placode || neural tube
Plexin repeat	0.00889	INHERITED FROM: otic placode || presumptive midbrain-hindbrain boundary || cranial placode
Erythroid transcription factor GATA-1	0.01812	INHERITED FROM: foregut || anterior dorsal lateral plate region || primordium || liver diverticulum || lateral plate mesoderm || cardiac progenitor cell || cardiac mesoderm
Glutathione peroxidase-like	0.04308	INHERITED FROM: foregut || anterior dorsal lateral plate region || eye primordium || presumptive paraxial mesoderm || paraxial mesoderm || presomitic mesoderm
VWC domain	0.04308	INHERITED FROM: axial mesoderm || prechordal plate || neural tube
Paired domain	0.04668	INHERITED FROM: primordium || anterior neural tube || posterior neural tube || neurogenic placode || cranial placode || neural tube
Group II chaperonin (CCT, TRIC), apical domain	0.04668	INHERITED FROM: anterior dorsal lateral plate region || lateral plate mesoderm || upper blastopore lip
Ubiquitin-related	0.07162	INHERITED FROM: upper blastopore lip
Group II chaperonin (CCT, TRIC), ATPase domain	0.09774	INHERITED FROM: anterior dorsal lateral plate region
Class I aldolase	0.09774	INHERITED FROM: primordium
Group II chaperonin (CCT, TRIC), intermediate domain	0.09965	INHERITED FROM: anterior dorsal lateral plate region || lateral plate mesoderm
Tandem AAA-ATPase domain	0.101	INHERITED FROM: blastopore || marginal zone || blastopore lip || upper blastopore lip
Tropomyosin	0.1435	INHERITED FROM: cardiac mesoderm
Classic zinc finger, C2H2	0.146	INHERITED FROM: lateral plate mesoderm || splanchnic layer of lateral plate mesoderm || presumptive rhombomere
Mannose 6-phosphate receptor domain	0.1701	INHERITED FROM: cement gland primordium
Transducin (alpha subunit), insertion domain	0.1887	INHERITED FROM: dorsal marginal zone
Alpha-macroglobulin receptor domain	0.1918	INHERITED FROM: foregut || midgut || hindgut
Globins	0.2192	INHERITED FROM: anterior dorsal lateral plate region || lateral plate mesoderm
AAT-like	0.2533	INHERITED FROM: presomitic mesoderm
Complement components	0.2964	INHERITED FROM: foregut || midgut || hindgut
Link domain	0.4034	INHERITED FROM: presomitic mesoderm
Nuclear receptor	0.5105	INHERITED FROM: foregut
LDL receptor-like module	0.6612	INHERITED FROM: hindgut
I set domains	0.8055	INHERITED FROM: optic vesicle

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 XA term (SPXA level: Moderately Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Homeodomain-like	0	DIRECT
Synuclein	0	DIRECT
SRF-like	0	DIRECT
PLP-binding barrel	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
14-3-3 protein	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
PriA/YqbF domain	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
"Winged helix" DNA-binding domain	0.00000000000000103	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.000000000000004116	DIRECT
RNA-binding domain, RBD	0.0000000001158	DIRECT
Cytokine	0.0000001021	DIRECT
Frizzled cysteine-rich domain	0.0000002856	DIRECT
HMG-box	0.00003725	DIRECT
Cystine-knot cytokines	0.0001689	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0002428	DIRECT
Sema domain	0.0002811	DIRECT
SAP domain	0.0005961	DIRECT
Cyclin-like	0.001227	INHERITED FROM: posterior neural tube
p53-like transcription factors	0.001227	INHERITED FROM: cranial placode || lower blastopore lip || neurogenic placode || foregut || ventral mesoderm || involuted ventral mesoderm || lung primordium || lung bud
Snake toxin-like	0.001318	INHERITED FROM: lateral plate mesoderm || anterior dorsal lateral plate region || dorsal lateral plate mesoderm || ventral mesoderm || involuted dorsal mesoderm
Orange domain-like	0.002116	INHERITED FROM: cranial placode || neurogenic placode || paraxial mesoderm
Plexin repeat	0.005757	INHERITED FROM: presumptive midbrain-hindbrain boundary || cranial placode || otic placode || involuted dorsal mesoderm
Eukaryotic type KH-domain (KH-domain type I)	0.009033	INHERITED FROM: lens placode
lambda repressor-like DNA-binding domains	0.01256	INHERITED FROM: presumptive midbrain-hindbrain boundary || cranial placode || neurogenic placode
GroEL-intermediate domain like	0.01708	INHERITED FROM: anterior dorsal lateral plate region
GroEL equatorial domain-like	0.01708	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.03767	INHERITED FROM: anterior dorsal lateral plate region
beta-beta-alpha zinc fingers	0.08533	INHERITED FROM: presumptive rhombomere || lateral plate mesoderm || splanchnic layer of lateral plate mesoderm
Mannose 6-phosphate receptor domain	0.1506	INHERITED FROM: cement gland primordium
F-box domain	0.156	INHERITED FROM: optic vesicle
Transducin (alpha subunit), insertion domain	0.1624	INHERITED FROM: dorsal marginal zone
Alpha-macroglobulin receptor domain	0.173	INHERITED FROM: foregut || hindgut || midgut
TIMP-like	0.1891	INHERITED FROM: stomodeal-hypophyseal primordium || foregut || prechordal plate || anterior neural tube
Globin-like	0.1931	INHERITED FROM: lateral plate mesoderm || anterior dorsal lateral plate region
EGF/Laminin	0.2	INHERITED FROM: axial mesoderm || dorsal marginal zone
Kazal-type serine protease inhibitors	0.2094	INHERITED FROM: axial mesoderm
Tropomyosin	0.2388	INHERITED FROM: cardiac mesoderm
FnI-like domain	0.2388	INHERITED FROM: axial mesoderm || prechordal plate || neural tube
DNA-binding domain	0.3125	INHERITED FROM: eye primordium
Protein kinase-like (PK-like)	0.4396	INHERITED FROM: lateral plate mesoderm
Terpenoid cyclases/Protein prenyltransferases	0.4881	INHERITED FROM: hindgut || midgut
LDL receptor-like module	0.6053	INHERITED FROM: hindgut
Nuclear receptor ligand-binding domain	0.6173	INHERITED FROM: foregut
E set domains	0.8941	INHERITED FROM: liver primordium || liver diverticulum

Supra-domains annotated to this XA term (SPXA 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)
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like	0	DIRECT
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	DIRECT
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0	DIRECT
47095,47095 47095 - HMG-box 47095 - HMG-box	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
49899,48726 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like	0	DIRECT
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.00000006498	DIRECT
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.00003396	DIRECT
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.0002811	DIRECT
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0002811	DIRECT
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.002116	INHERITED FROM: cranial placode || neurogenic placode || paraxial mesoderm
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like	0.009829	INHERITED FROM: marginal zone || blastopore || blastopore lip || upper blastopore lip
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.015	INHERITED FROM: neurogenic placode
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.015	INHERITED FROM: anterior dorsal lateral plate region
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0.015	INHERITED FROM: cranial placode
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.01542	INHERITED FROM: presumptive midbrain-hindbrain boundary || cranial placode || neurogenic placode
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.03917	INHERITED FROM: anterior dorsal lateral plate region
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.05865	INHERITED FROM: dorsal marginal zone
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.06944	INHERITED FROM: presumptive rhombomere || lateral plate mesoderm || splanchnic layer of lateral plate mesoderm
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.08186	INHERITED FROM: circumblastoporal collar
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.08532	INHERITED FROM: optic vesicle
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.1307	INHERITED FROM: foregut
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1624	INHERITED FROM: dorsal marginal zone
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1646	INHERITED FROM: blastopore || blastopore lip || upper blastopore lip
46689,46689 46689 - Homeodomain-like 46689 - Homeodomain-like	0.2227	INHERITED FROM: optic vesicle
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.2443	INHERITED FROM: non-involuting marginal zone
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.4149	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.6298	INHERITED FROM: non-involuting marginal zone

Supra-domains annotated to this XA term (SPXA 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)
47220,47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0	DIRECT
49899,48726,49265 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin 49265 - Fibronectin type III	0	DIRECT
103647,103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat	0	DIRECT
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain	0.003285	INHERITED FROM: circumblastoporal collar
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.015	INHERITED FROM: anterior dorsal lateral plate region
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0.015	INHERITED FROM: cranial placode
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.03767	INHERITED FROM: non-involuting marginal zone
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.03767	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III	0.08532	INHERITED FROM: optic vesicle
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.08863	INHERITED FROM: paraxial mesoderm || neural tube || presomitic mesoderm || dorsal marginal zone
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	1	INHERITED FROM: splanchnic layer of lateral plate mesoderm

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.