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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)
Synuclein	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
SRF-like	0	DIRECT
Homeodomain-like	0	DIRECT
PLP-binding barrel	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
14-3-3 protein	0	DIRECT
PriA/YqbF domain	0	DIRECT
GINS helical bundle-like	0	DIRECT
"Winged helix" DNA-binding domain	0.000000000000003915	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.00000000000008038	DIRECT
RNA-binding domain, RBD	0.00000000003789	DIRECT
Cytokine	0.0000003178	DIRECT
Frizzled cysteine-rich domain	0.0000009833	DIRECT
HMG-box	0.00003697	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0003486	DIRECT
Cystine-knot cytokines	0.0006241	DIRECT
Sema domain	0.0007629	DIRECT
Snake toxin-like	0.002824	INHERITED FROM: dorsal lateral plate mesoderm || involuted dorsal mesoderm || ventral mesoderm || lateral plate mesoderm
Cyclin-like	0.003439	INHERITED FROM: posterior neural tube
p53-like transcription factors	0.003439	INHERITED FROM: neurogenic placode || cranial placode || lung bud || foregut || involuted ventral mesoderm || lower blastopore lip || lung primordium
Orange domain-like	0.004053	INHERITED FROM: presomitic mesoderm || paraxial mesoderm || neural tube || cranial placode || lateral plate mesoderm || chordoneural hinge
Plexin repeat	0.01335	INHERITED FROM: otic placode || cranial placode || involuted dorsal mesoderm || presumptive midbrain-hindbrain boundary || liver primordium
lambda repressor-like DNA-binding domains	0.02445	INHERITED FROM: neurogenic placode || cranial placode || presumptive midbrain-hindbrain boundary
GroEL-intermediate domain like	0.02881	INHERITED FROM: anterior dorsal lateral plate region
GroEL equatorial domain-like	0.02881	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.06008	INHERITED FROM: anterior dorsal lateral plate region
Transducin (alpha subunit), insertion domain	0.09425	INHERITED FROM: dorsal marginal zone
beta-beta-alpha zinc fingers	0.1572	INHERITED FROM: splanchnic layer of lateral plate mesoderm || presumptive rhombomere
Mannose 6-phosphate receptor domain	0.2001	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.2237	INHERITED FROM: midgut || hindgut || foregut
Globin-like	0.2553	INHERITED FROM: anterior dorsal lateral plate region
TIMP-like	0.2581	INHERITED FROM: foregut || anterior neural tube || prechordal plate || stomodeal-hypophyseal primordium
EGF/Laminin	0.2637	INHERITED FROM: axial mesoderm
FnI-like domain	0.2718	INHERITED FROM: neural tube || prechordal plate
Kazal-type serine protease inhibitors	0.2841	INHERITED FROM: axial mesoderm
Tropomyosin	0.3249	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.3849	INHERITED FROM: eye primordium
LDL receptor-like module	0.5525	INHERITED FROM: hindgut
Terpenoid cyclases/Protein prenyltransferases	0.5722	INHERITED FROM: midgut || hindgut

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)
Extracellular domain of cell surface receptors	0	DIRECT
Troponin I	0	DIRECT
SRF-like	0	DIRECT
SH3BGR (SH3-binding, glutamic acid-rich protein-like)	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
Homeodomain	0	DIRECT
14-3-3 protein	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	DIRECT
Alanine racemase-like, N-terminal domain	0	DIRECT
Eukaryotic ODC-like	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
Guanido kinase catalytic domain	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
Hedgehog (development protein), N-terminal signaling domain	0	DIRECT
Ran-binding domain	0	DIRECT
Noggin	0	DIRECT
Pointed domain	0	DIRECT
Synuclein	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.0000000000004082	DIRECT
Forkhead DNA-binding domain	0.000000000000945	DIRECT
Canonical RBD	0.00000000001571	DIRECT
ets domain	0.00000004644	DIRECT
Transforming growth factor (TGF)-beta	0.000001287	DIRECT
Frizzled cysteine-rich domain	0.000001349	DIRECT
HMG-box	0.00006034	DIRECT
Sema domain	0.0003709	DIRECT
T-box	0.0004069	DIRECT
POU-specific domain	0.001008	INHERITED FROM: neural tube || neurogenic placode || presumptive midbrain-hindbrain boundary
Cyclin	0.001904	INHERITED FROM: posterior neural tube || anterior neural tube
LIM domain	0.003408	INHERITED FROM: cranial placode
Hairy Orange domain	0.004094	INHERITED FROM: presomitic mesoderm || paraxial mesoderm || neural tube || cranial placode || lateral plate mesoderm || chordoneural hinge
P4 origin-binding domain-like	0.005582	INHERITED FROM: otic placode || neural tube || optic vesicle || neurogenic placode || cranial placode
Cell cycle control phosphatase, catalytic domain	0.005582	INHERITED FROM: neural tube
Plexin repeat	0.01602	INHERITED FROM: otic placode || cranial placode || presumptive midbrain-hindbrain boundary || liver primordium
Eukaryotic type KH-domain (KH-domain type I)	0.02394	INHERITED FROM: upper blastopore lip
Erythroid transcription factor GATA-1	0.02395	INHERITED FROM: hematopoietic stem cell || cardiac progenitor cell || liver diverticulum || primordium || anterior dorsal lateral plate region || lateral plate mesoderm || cardiac mesoderm
VWC domain	0.03025	INHERITED FROM: neural tube || prechordal plate
Glutathione peroxidase-like	0.05815	INHERITED FROM: presomitic mesoderm || paraxial mesoderm || presumptive paraxial mesoderm || foregut || eye primordium
Group II chaperonin (CCT, TRIC), apical domain	0.0596	INHERITED FROM: upper blastopore lip || anterior dorsal lateral plate region || lateral plate mesoderm
Paired domain	0.0596	INHERITED FROM: neural tube || neurogenic placode || cranial placode || primordium || posterior neural tube || anterior neural tube
Tandem AAA-ATPase domain	0.07475	INHERITED FROM: blastopore || upper blastopore lip || marginal zone || blastopore lip
Transducin (alpha subunit), insertion domain	0.09666	INHERITED FROM: dorsal marginal zone
Group II chaperonin (CCT, TRIC), intermediate domain	0.1172	INHERITED FROM: anterior dorsal lateral plate region || lateral plate mesoderm
Class I aldolase	0.1178	INHERITED FROM: primordium
Group II chaperonin (CCT, TRIC), ATPase domain	0.1178	INHERITED FROM: anterior dorsal lateral plate region
Classic zinc finger, C2H2	0.1787	INHERITED FROM: splanchnic layer of lateral plate mesoderm || presumptive rhombomere
Tropomyosin	0.1875	INHERITED FROM: cardiac mesoderm
Mannose 6-phosphate receptor domain	0.1999	INHERITED FROM: cement gland primordium
Arginine methyltransferase	0.2209	INHERITED FROM: optic vesicle
Alpha-macroglobulin receptor domain	0.2209	INHERITED FROM: midgut || hindgut || foregut
Globins	0.2566	INHERITED FROM: anterior dorsal lateral plate region
Complement components	0.331	INHERITED FROM: midgut || hindgut
Link domain	0.4452	INHERITED FROM: presomitic mesoderm
LDL receptor-like module	0.5763	INHERITED FROM: hindgut
I set domains	0.7362	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
GINS helical bundle-like	0	DIRECT
PLP-binding barrel	0	DIRECT
PriA/YqbF domain	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
SRF-like	0	DIRECT
Synuclein	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
14-3-3 protein	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
"Winged helix" DNA-binding domain	0.000000000000002689	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.00000000000005531	DIRECT
RNA-binding domain, RBD	0.0000000000262	DIRECT
Cytokine	0.0000002233	DIRECT
Frizzled cysteine-rich domain	0.0000006937	DIRECT
HMG-box	0.00002685	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0002599	DIRECT
Cystine-knot cytokines	0.0004683	DIRECT
Sema domain	0.0005743	DIRECT
Snake toxin-like	0.00217	INHERITED FROM: lateral plate mesoderm || involuted dorsal mesoderm || ventral mesoderm || dorsal lateral plate mesoderm
p53-like transcription factors	0.00264	INHERITED FROM: foregut || cranial placode || neurogenic placode || lung primordium || lower blastopore lip || primordium || lung bud || involuted ventral mesoderm
Cyclin-like	0.00264	INHERITED FROM: posterior neural tube
Orange domain-like	0.003119	INHERITED FROM: lateral plate mesoderm || neural tube || cranial placode || presomitic mesoderm || paraxial mesoderm || chordoneural hinge
Plexin repeat	0.0105	INHERITED FROM: otic placode || cranial placode || involuted dorsal mesoderm || liver primordium || presumptive midbrain-hindbrain boundary
lambda repressor-like DNA-binding domains	0.01948	INHERITED FROM: cranial placode || presumptive midbrain-hindbrain boundary || neurogenic placode
GroEL-intermediate domain like	0.02306	INHERITED FROM: anterior dorsal lateral plate region
GroEL equatorial domain-like	0.02306	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.04955	INHERITED FROM: anterior dorsal lateral plate region
Transducin (alpha subunit), insertion domain	0.07958	INHERITED FROM: dorsal marginal zone
F-box domain	0.1367	INHERITED FROM: optic vesicle
beta-beta-alpha zinc fingers	0.1371	INHERITED FROM: presumptive rhombomere || splanchnic layer of lateral plate mesoderm
Mannose 6-phosphate receptor domain	0.1768	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.1991	INHERITED FROM: hindgut || foregut || midgut
Globin-like	0.2285	INHERITED FROM: lateral plate mesoderm || anterior dorsal lateral plate region || hematopoietic stem cell
TIMP-like	0.2311	INHERITED FROM: foregut || stomodeal-hypophyseal primordium || axial mesoderm || prechordal plate || anterior neural tube
EGF/Laminin	0.2366	INHERITED FROM: axial mesoderm
FnI-like domain	0.2443	INHERITED FROM: neural tube || prechordal plate
Kazal-type serine protease inhibitors	0.256	INHERITED FROM: axial mesoderm
Tropomyosin	0.2952	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.3532	INHERITED FROM: eye primordium
LDL receptor-like module	0.5158	INHERITED FROM: hindgut
Terpenoid cyclases/Protein prenyltransferases	0.5351	INHERITED FROM: hindgut || midgut
E set domains	0.9015	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)
49899,48726 49899 - Concanavalin A-like lectins/glucanases 48726 - Immunoglobulin	0	DIRECT
51419,50621 51419 - PLP-binding barrel 50621 - Alanine racemase C-terminal domain-like	0	DIRECT
103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	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
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like	0	DIRECT
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like	0	DIRECT
48034,55931 48034 - Guanido kinase N-terminal domain 55931 - Glutamine synthetase/guanido kinase	0	DIRECT
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.0000002532	DIRECT
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.00002589	DIRECT
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0005743	DIRECT
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.0005743	DIRECT
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.003119	INHERITED FROM: lateral plate mesoderm || neural tube || cranial placode || presomitic mesoderm || paraxial mesoderm || chordoneural hinge
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like	0.01269	INHERITED FROM: upper blastopore lip || marginal zone || vegetal yolk mass || blastopore lip || blastopore
48592,54849 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like	0.0198	INHERITED FROM: anterior dorsal lateral plate region
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0.0198	INHERITED FROM: cranial placode
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.02258	INHERITED FROM: presumptive midbrain-hindbrain boundary || neurogenic placode
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I)	0.03979	INHERITED FROM: neurogenic placode
54849,52029 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.05013	INHERITED FROM: anterior dorsal lateral plate region
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.06351	INHERITED FROM: non-involuting marginal zone
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.07958	INHERITED FROM: dorsal marginal zone
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.08865	INHERITED FROM: foregut
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.092	INHERITED FROM: lateral plate mesoderm || presumptive rhombomere || splanchnic layer of lateral plate mesoderm
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.09806	INHERITED FROM: dorsal marginal zone
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.1032	INHERITED FROM: optic vesicle
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1071	INHERITED FROM: circumblastoporal collar
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1688	INHERITED FROM: upper blastopore lip || blastopore lip || blastopore
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.4683	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.4951	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)
103647,103647,49899 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
103647,103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat	0	DIRECT
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
57603,57603,57603 57603 - FnI-like domain 57603 - FnI-like domain 57603 - FnI-like domain	0.004502	INHERITED FROM: neural tube || circumblastoporal collar
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.01013	INHERITED FROM: non-involuting marginal zone
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0.0198	INHERITED FROM: cranial placode
48592,54849,52029 48592 - GroEL equatorial domain-like 54849 - GroEL-intermediate domain like 52029 - GroEL apical domain-like	0.0198	INHERITED FROM: anterior dorsal lateral plate region
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.04955	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat	0.05013	INHERITED FROM: chordoneural hinge
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III	0.1032	INHERITED FROM: optic vesicle
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.1044	INHERITED FROM: presomitic mesoderm || paraxial 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.