Mammalian Phenotype (MP): abnormal definitive hematopoiesis

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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).

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Root: MP Hierarchy (mammalian/mouse phenotype from MGI_4.41)

Shortest distance to current term (+ for parents, - for children) MP term [MP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + + + 6: mammalian phenotype [MP:0000001] <29>

+ + + + 4: hematopoietic system phenotype [MP:0005397] <2> (72|102) (78|63|30)

+ + + 3: abnormal hematopoietic system morphology/development [MP:0002396] <5> (58|86) (66|47|21)

+ + + 3: abnormal hematopoietic cell morphology [MP:0013656] <9> (49|77) (60|43|18)

+ + 2: abnormal blood cell morphology [MP:0013657] <4> (31|49) (37|35|14)

+ + 2: abnormal blood cell morphology/development [MP:0002429] <3> (26|35) (28|24|9)

+ 1: abnormal hemopoiesis [MP:0013693] <2> (25|34) (27|24|9)

0: abnormal definitive hematopoiesis [MP:0002123] <4> (24|34) (26|24|9)

- 1: abnormal leukopoiesis [MP:0005460] <3> (19|28) (21|18|8)

- 1: abnormal common myeloid progenitor cell morphology [MP:0006410] <2> (1|1) (1|2|0)

- 1: abnormal erythropoiesis [MP:0000245] (0|0) (0|0|0)

- 1: extramedullary hematopoiesis [MP:0000240] (2|2) (2|1|0)

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
SPOC domain-like	0	Direct
SH2 domain	0	Direct
STAT	0	Direct
Transcription factor STAT-4 N-domain	0	Direct
PsbU/PolX domain-like	0	Direct
p53-like transcription factors	0.000000001415	Direct
4-helical cytokines	0.000007326	Direct
TNF receptor-like	0.000008144	Direct
DNA polymerase beta, N-terminal domain-like	0.0004023	Direct
DEATH domain	0.0008489	Direct
Cyclin-like	0.0009455	Direct
BRCT domain	0.001416	Inherited
Bcl-2 inhibitors of programmed cell death	0.001878	Inherited
Cysteine-rich domain	0.002195	Inherited
E2F-DP heterodimerization region	0.003844	Inherited
Notch domain	0.007393	Inherited
DNA/RNA polymerases	0.03879	Inherited
Nucleotidyltransferase	0.06466	Inherited
SH3-domain	0.1058	Inherited
SET domain	0.136	Inherited
DBL homology domain (DH-domain)	0.2774	Inherited
Ankyrin repeat	0.2999	Inherited
Calponin-homology domain, CH-domain	0.6774	Inherited
SMAD/FHA domain	0.8821	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
STAT DNA-binding domain	0	Direct
RUNT domain	0	Direct
DNA polymerase beta-like	0	Direct
Transcription factor STAT-4 N-domain	0	Direct
STAT	0	Direct
SH2 domain	0	Direct
DNA polymerase beta-like, second domain	0	Direct
Short-chain cytokines	0.00000008818	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.0000008423	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.000005871	Direct
TNF receptor-like	0.00003121	Direct
ets domain	0.0002295	Direct
V set domains (antibody variable domain-like)	0.0002622	Direct
DNA polymerase beta, N-terminal domain-like	0.0002685	Direct
PLC-like (P variant)	0.0008246	Direct
E2F dimerization segment	0.001096	Inherited
Cyclin	0.001103	Inherited
Bcl-2 inhibitors of programmed cell death	0.001369	Inherited
DEATH domain, DD	0.001452	Inherited
Pointed domain	0.002811	Inherited
Notch domain	0.005454	Inherited
Pleckstrin-homology domain (PH domain)	0.009554	Inherited
Cell cycle transcription factor e2f-dp	0.009921	Inherited
DNA polymerase I	0.01194	Inherited
Interferon regulatory factor 3 (IRF3), transactivation domain	0.02115	Inherited
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.0222	Inherited
MATH domain	0.08428	Inherited
Higher-molecular-weight phosphotyrosine protein phosphatases	0.09671	Inherited
SH3-domain	0.1127	Inherited
FHA domain	0.1789	Inherited
DBL homology domain (DH-domain)	0.2704	Inherited
Ankyrin repeat	0.3001	Inherited
Calponin-homology domain, CH-domain	0.6727	Inherited
Myb/SANT domain	0.9223	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
SPOC domain-like	0	Direct
SH2 domain	0	Direct
PsbU/PolX domain-like	0	Direct
STAT	0	Direct
Transcription factor STAT-4 N-domain	0	Direct
p53-like transcription factors	0.0000000005272	Direct
4-helical cytokines	0.000003169	Direct
TNF receptor-like	0.000003542	Direct
DNA polymerase beta, N-terminal domain-like	0.0002102	Direct
DEATH domain	0.0004595	Direct
Cyclin-like	0.0005139	Direct
BRCT domain	0.0007901	Direct
Bcl-2 inhibitors of programmed cell death	0.001065	Inherited
Cysteine-rich domain	0.001251	Inherited
E2F-DP heterodimerization region	0.002259	Inherited
Notch domain	0.004543	Inherited
DNA/RNA polymerases	0.02685	Inherited
Nucleotidyltransferase	0.04691	Inherited
SH3-domain	0.08038	Inherited
SET domain	0.1065	Inherited
DBL homology domain (DH-domain)	0.2354	Inherited
Ankyrin repeat	0.2566	Inherited
Acyl-CoA N-acyltransferases (Nat)	0.4238	Inherited
beta-beta-alpha zinc fingers	0.5851	Inherited
Calponin-homology domain, CH-domain	0.6355	Inherited
SMAD/FHA domain	0.8538	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0	Direct
47802,81585 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like	0	Direct
81585,81301 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase	0	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0	Direct
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0	Direct
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0	Direct
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain)	0	Direct
55550,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.00000002272	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0.0000001932	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.0000005048	Direct
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.000003365	Direct
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like)	0.00002483	Direct
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0.00003043	Direct
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.0001039	Direct
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0001778	Direct
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.0008744	Direct
56112,56112 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.001065	Inherited
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.001065	Inherited
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0.001326	Inherited
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0.001326	Inherited
46785,144074 46785 - "Winged helix" DNA-binding domain 144074 - E2F-DP heterodimerization region	0.002259	Inherited
57850,49599 57850 - RING/U-box 49599 - TRAF domain-like	0.02845	Inherited
48065,50729 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0.2052	Inherited
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.6602	Inherited

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50729,50044,55550 50729 - PH domain-like 50044 - SH3-domain 55550 - SH2 domain	0	Direct
47802,81585,81301 47802 - DNA polymerase beta, N-terminal domain-like 81585 - PsbU/PolX domain-like 81301 - Nucleotidyltransferase	0	Direct
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0	Direct
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0	Direct
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0	Direct
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0	Direct
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
50044,55550,56112 50044 - SH3-domain 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.00001717	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0.001326	Inherited

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Mammalian Phenotype (MP): abnormal definitive hematopoiesis

Superfamily

Family

Supra-domain (including individual superfamily)