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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)
Guanido kinase N-terminal domain	0	DIRECT
GINS helical bundle-like	0	DIRECT
LysM domain	0	DIRECT
PLP-binding barrel	0	DIRECT
Synuclein	0	DIRECT
SRF-like	0	DIRECT
PriA/YqbF domain	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
Homeodomain-like	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
"Winged helix" DNA-binding domain	0.00000000000002291	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.00000000000005039	DIRECT
RNA-binding domain, RBD	0.000000000003907	DIRECT
Cytokine	0.0000003455	DIRECT
Frizzled cysteine-rich domain	0.000001083	DIRECT
HMG-box	0.00004217	DIRECT
Cystine-knot cytokines	0.000122	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0002029	DIRECT
Sema domain	0.000826	DIRECT
Snake toxin-like	0.002973	INHERITED FROM: involuted dorsal mesoderm || ventral mesoderm || lateral plate mesoderm
p53-like transcription factors	0.003758	INHERITED FROM: lung primordium || lower blastopore lip || foregut || cranial placode || lung bud || involuted ventral mesoderm || neurogenic placode
Orange domain-like	0.004203	INHERITED FROM: neural tube || lateral plate mesoderm || cranial placode || presomitic mesoderm || chordoneural hinge || paraxial mesoderm
GroEL-intermediate domain like	0.004203	INHERITED FROM: anterior dorsal lateral plate region
GroEL equatorial domain-like	0.004203	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.01335	INHERITED FROM: anterior dorsal lateral plate region
Plexin repeat	0.01431	INHERITED FROM: involuted dorsal mesoderm || cranial placode || presumptive midbrain-hindbrain boundary || liver primordium || otic placode
lambda repressor-like DNA-binding domains	0.02577	INHERITED FROM: cranial placode || presumptive midbrain-hindbrain boundary || neurogenic placode
Transducin (alpha subunit), insertion domain	0.09808	INHERITED FROM: dorsal marginal zone
beta-beta-alpha zinc fingers	0.1256	INHERITED FROM: presumptive rhombomere || splanchnic layer of lateral plate mesoderm
TIMP-like	0.1294	INHERITED FROM: stomodeal-hypophyseal primordium || foregut || prechordal plate
Mannose 6-phosphate receptor domain	0.2055	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.2288	INHERITED FROM: hindgut || foregut || midgut
Globin-like	0.2623	INHERITED FROM: hematopoietic stem cell || anterior dorsal lateral plate region
FnI-like domain	0.2815	INHERITED FROM: prechordal plate
EGF/Laminin	0.2819	INHERITED FROM: axial mesoderm
Kazal-type serine protease inhibitors	0.293	INHERITED FROM: axial mesoderm
Tropomyosin	0.3357	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.3928	INHERITED FROM: eye primordium
LDL receptor-like module	0.5654	INHERITED FROM: hindgut
Terpenoid cyclases/Protein prenyltransferases	0.5803	INHERITED FROM: hindgut || midgut

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)
Alanine racemase-like, N-terminal domain	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain	0	DIRECT
SH3BGR (SH3-binding, glutamic acid-rich protein-like)	0	DIRECT
Hedgehog (development protein), N-terminal signaling domain	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
LysM domain	0	DIRECT
Ran-binding domain	0	DIRECT
SRF-like	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
Noggin	0	DIRECT
Eukaryotic ODC-like	0	DIRECT
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain	0	DIRECT
Guanido kinase catalytic domain	0	DIRECT
Pointed domain	0	DIRECT
Homeodomain	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
Synuclein	0	DIRECT
14-3-3 protein	0	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.0000000000002587	DIRECT
Canonical RBD	0.000000000001107	DIRECT
Forkhead DNA-binding domain	0.000000000001163	DIRECT
ets domain	0.00000005123	DIRECT
Transforming growth factor (TGF)-beta	0.0000006152	DIRECT
Frizzled cysteine-rich domain	0.000001489	DIRECT
HMG-box	0.00006854	DIRECT
Sema domain	0.0004016	DIRECT
T-box	0.0004338	DIRECT
POU-specific domain	0.001066	INHERITED FROM: neural tube || presumptive midbrain-hindbrain boundary || neurogenic placode
LIM domain	0.003692	INHERITED FROM: cranial placode
Hairy Orange domain	0.004263	INHERITED FROM: neural tube || lateral plate mesoderm || cranial placode || presomitic mesoderm || chordoneural hinge || paraxial mesoderm
Cell cycle control phosphatase, catalytic domain	0.005767	INHERITED FROM: neural tube
P4 origin-binding domain-like	0.005767	INHERITED FROM: neural tube || optic vesicle || cranial placode || neurogenic placode || otic placode
Group II chaperonin (CCT, TRIC), apical domain	0.0105	INHERITED FROM: anterior dorsal lateral plate region
Group II chaperonin (CCT, TRIC), intermediate domain	0.01557	INHERITED FROM: anterior dorsal lateral plate region
Plexin repeat	0.01715	INHERITED FROM: cranial placode || presumptive midbrain-hindbrain boundary || liver primordium || otic placode
Erythroid transcription factor GATA-1	0.02477	INHERITED FROM: cardiac mesoderm || hematopoietic stem cell || lateral plate mesoderm || anterior dorsal lateral plate region || primordium || liver diverticulum || cardiac progenitor cell
Eukaryotic type KH-domain (KH-domain type I)	0.02557	INHERITED FROM: upper blastopore lip
VWC domain	0.03149	INHERITED FROM: neural tube || prechordal plate
Glutathione peroxidase-like	0.06008	INHERITED FROM: presumptive paraxial mesoderm || foregut || eye primordium || presomitic mesoderm || paraxial mesoderm
Paired domain	0.0614	INHERITED FROM: posterior neural tube || neural tube || cranial placode || primordium || neurogenic placode || anterior neural tube
Tandem AAA-ATPase domain	0.08095	INHERITED FROM: upper blastopore lip || blastopore || blastopore lip || marginal zone || vegetal yolk mass
Transducin (alpha subunit), insertion domain	0.1001	INHERITED FROM: dorsal marginal zone
Classic zinc finger, C2H2	0.1184	INHERITED FROM: presumptive rhombomere || splanchnic layer of lateral plate mesoderm
Class I aldolase	0.1214	INHERITED FROM: primordium
Tropomyosin	0.1946	INHERITED FROM: cardiac mesoderm
Mannose 6-phosphate receptor domain	0.2053	INHERITED FROM: cement gland primordium
Arginine methyltransferase	0.2261	INHERITED FROM: optic vesicle
Alpha-macroglobulin receptor domain	0.2261	INHERITED FROM: hindgut || foregut || midgut
Globins	0.2638	INHERITED FROM: hematopoietic stem cell || anterior dorsal lateral plate region
Complement components	0.3386	INHERITED FROM: hindgut || midgut
LDL receptor-like module	0.5887	INHERITED FROM: hindgut
I set domains	0.7491	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)
LysM domain	0	DIRECT
14-3-3 protein	0	DIRECT
PriA/YqbF domain	0	DIRECT
Hedgehog/DD-peptidase	0	DIRECT
Homeodomain-like	0	DIRECT
Alanine racemase C-terminal domain-like	0	DIRECT
Cysteine-rich DNA binding domain, (DM domain)	0	DIRECT
GINS helical bundle-like	0	DIRECT
Synuclein	0	DIRECT
PLP-binding barrel	0	DIRECT
Guanido kinase N-terminal domain	0	DIRECT
SRF-like	0	DIRECT
"Winged helix" DNA-binding domain	0.00000000000001593	DIRECT
HLH, helix-loop-helix DNA-binding domain	0.00000000000003505	DIRECT
RNA-binding domain, RBD	0.000000000002726	DIRECT
Cytokine	0.0000002453	DIRECT
Frizzled cysteine-rich domain	0.0000007728	DIRECT
HMG-box	0.0000309	DIRECT
Cystine-knot cytokines	0.00009041	DIRECT
Glucocorticoid receptor-like (DNA-binding domain)	0.0001513	DIRECT
Sema domain	0.0006265	DIRECT
Snake toxin-like	0.002295	INHERITED FROM: dorsal lateral plate mesoderm || ventral mesoderm || lateral plate mesoderm || involuted dorsal mesoderm
p53-like transcription factors	0.002902	INHERITED FROM: lung primordium || involuted ventral mesoderm || primordium || foregut || lung bud || neurogenic placode || lower blastopore lip || cranial placode
GroEL-intermediate domain like	0.003255	INHERITED FROM: anterior dorsal lateral plate region
Orange domain-like	0.003255	INHERITED FROM: presomitic mesoderm || chordoneural hinge || lateral plate mesoderm || neural tube || paraxial mesoderm || cranial placode
GroEL equatorial domain-like	0.003255	INHERITED FROM: anterior dorsal lateral plate region
GroEL apical domain-like	0.01053	INHERITED FROM: anterior dorsal lateral plate region
Plexin repeat	0.01129	INHERITED FROM: liver primordium || presumptive midbrain-hindbrain boundary || involuted dorsal mesoderm || otic placode || cranial placode
lambda repressor-like DNA-binding domains	0.02061	INHERITED FROM: presumptive midbrain-hindbrain boundary || neurogenic placode || cranial placode
Transducin (alpha subunit), insertion domain	0.083	INHERITED FROM: dorsal marginal zone
beta-beta-alpha zinc fingers	0.1081	INHERITED FROM: presumptive rhombomere || splanchnic layer of lateral plate mesoderm
TIMP-like	0.1116	INHERITED FROM: foregut || stomodeal-hypophyseal primordium || prechordal plate
F-box domain	0.1445	INHERITED FROM: optic vesicle
Mannose 6-phosphate receptor domain	0.1817	INHERITED FROM: cement gland primordium
Alpha-macroglobulin receptor domain	0.2037	INHERITED FROM: hindgut || foregut || midgut
Globin-like	0.2351	INHERITED FROM: hematopoietic stem cell || lateral plate mesoderm || anterior dorsal lateral plate region
FnI-like domain	0.2537	INHERITED FROM: neural tube || prechordal plate
EGF/Laminin	0.2541	INHERITED FROM: axial mesoderm
Kazal-type serine protease inhibitors	0.2649	INHERITED FROM: axial mesoderm
Tropomyosin	0.3059	INHERITED FROM: cardiac mesoderm
DNA-binding domain	0.3621	INHERITED FROM: eye primordium
LDL receptor-like module	0.5293	INHERITED FROM: hindgut
Terpenoid cyclases/Protein prenyltransferases	0.5447	INHERITED FROM: hindgut || midgut
E set domains	0.9339	INHERITED FROM: 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)
103647,103647 103647 - TSP type-3 repeat 103647 - TSP type-3 repeat	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
54534,54534 54534 - FKBP-like 54534 - FKBP-like	0	DIRECT
47095,47095 47095 - HMG-box 47095 - HMG-box	0	DIRECT
52540,53254 52540 - P-loop containing nucleoside triphosphate hydrolases 53254 - Phosphoglycerate mutase-like	0	DIRECT
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
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-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)	0.0000003013	DIRECT
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.0000299	DIRECT
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0.0006265	DIRECT
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0006265	DIRECT
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.003255	INHERITED FROM: presomitic mesoderm || chordoneural hinge || lateral plate mesoderm || neural tube || paraxial mesoderm || cranial placode
90209,90209 90209 - Ran binding protein zinc finger-like 90209 - Ran binding protein zinc finger-like	0.01302	INHERITED FROM: blastopore || blastopore lip || marginal zone || upper blastopore lip || vegetal yolk mass
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0.02047	INHERITED FROM: cranial placode
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.02047	INHERITED FROM: neurogenic placode
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.02371	INHERITED FROM: presumptive midbrain-hindbrain boundary || neurogenic placode
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.06421	INHERITED FROM: presumptive rhombomere || lateral plate mesoderm || splanchnic layer of lateral plate mesoderm
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.06647	INHERITED FROM: non-involuting marginal zone
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.083	INHERITED FROM: dorsal marginal zone
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1053	INHERITED FROM: dorsal marginal zone
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.1063	INHERITED FROM: optic vesicle
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1116	INHERITED FROM: circumblastoporal collar
52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.1797	INHERITED FROM: blastopore || blastopore lip || upper blastopore lip || vegetal yolk mass
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.4783	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.5042	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	0.004661	INHERITED FROM: circumblastoporal collar || neural tube
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.01053	INHERITED FROM: non-involuting marginal zone
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0.02047	INHERITED FROM: cranial placode
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.03668	INHERITED FROM: non-neurogenic ectodermal placode
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.05133	INHERITED FROM: presomitic mesoderm || dorsal marginal zone
48371,48371,48371 48371 - ARM repeat 48371 - ARM repeat 48371 - ARM repeat	0.05182	INHERITED FROM: chordoneural hinge
48726,49265,49265 48726 - Immunoglobulin 49265 - Fibronectin type III 49265 - Fibronectin type III	0.1063	INHERITED FROM: optic vesicle
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.1072	INHERITED FROM: presomitic mesoderm || dorsal marginal zone || paraxial mesoderm
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.9571	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.