CTD Diseases (CD): Digestive System Neoplasms

Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype 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. Biomedical ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology
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 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 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
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 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 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 displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology
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
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
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.
UniProtKB KeyWords (KW) Ontology
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).
CTD Diseases (CD) Ontology
CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
CTD Chemicals (CC) Ontology
CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
DNA repair protein MutS, domain III	0	Direct
RGC domain-like	0	Direct
ABC transporter transmembrane region	0.00004475	Direct
Multidrug efflux transporter AcrB transmembrane domain	0.0001531	Direct
Notch domain	0.002363	Inherited
Bcl-2 inhibitors of programmed cell death	0.007984	Inherited
Metallothionein	0.0167	Inherited
Frizzled cysteine-rich domain	0.02276	Inherited
SMAD MH1 domain	0.03373	Inherited
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0.03477	Inherited
Ribosomal protein S5 domain 2-like	0.0701	Inherited
Growth factor receptor domain	0.1246	Inherited
Serum albumin-like	0.1636	Inherited
Orange domain-like	0.1636	Inherited
L domain-like	0.327	Inherited
ARM repeat	0.9619	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
DNA repair protein MutS, domain III	0	Direct
Multidrug efflux transporter AcrB transmembrane domain	0	Direct
RGC domain	0	Direct
DEATH effector domain, DED	0	Direct
ABC transporter ATPase domain-like	0.0000004265	Direct
ABC transporter transmembrane region	0.0003453	Direct
DNA gyrase/MutL, second domain	0.0005367	Direct
DNA gyrase/MutL, N-terminal domain	0.0005367	Direct
Notch domain	0.002045	Inherited
L domain	0.00224	Inherited
Interferons/interleukin-10 (IL-10)	0.003167	Inherited
Bcl-2 inhibitors of programmed cell death	0.00674	Inherited
Metallothionein	0.01417	Inherited
Frizzled cysteine-rich domain	0.0219	Inherited
SMAD MH1 domain	0.03044	Inherited
SMAD domain	0.03044	Inherited
Growth factor receptor domain	0.03757	Inherited
EGF-type module	0.03981	Inherited
Fibronectin type II module	0.04444	Inherited
Serum albumin-like	0.1481	Inherited
Hairy Orange domain	0.1481	Inherited
Protein kinases, catalytic subunit	0.1685	Inherited
Prefoldin	0.2576	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
RGC domain-like	0	Direct
DNA repair protein MutS, domain III	0	Direct
ABC transporter transmembrane region	0.00002369	Direct
Multidrug efflux transporter AcrB transmembrane domain	0.00008759	Direct
Notch domain	0.00161	Inherited
Bcl-2 inhibitors of programmed cell death	0.005808	Inherited
Metallothionein	0.01245	Inherited
Frizzled cysteine-rich domain	0.01733	Inherited
SMAD MH1 domain	0.02636	Inherited
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0.02717	Inherited
PGBD-like	0.05347	Inherited
Ribosomal protein S5 domain 2-like	0.05704	Inherited
p53-like transcription factors	0.1003	Inherited
Protein kinase-like (PK-like)	0.1012	Inherited
Growth factor receptor domain	0.1055	Inherited
Lipase/lipooxygenase domain (PLAT/LH2 domain)	0.1142	Inherited
Orange domain-like	0.1405	Inherited
Serum albumin-like	0.1405	Inherited
L domain-like	0.2944	Inherited
ARM repeat	0.9464	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
52058,52047 52058 - L domain-like 52047 - RNI-like	0	Direct
48334,52540 48334 - DNA repair protein MutS, domain III 52540 - P-loop containing nucleoside triphosphate hydrolases	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
90193,90193 90193 - Notch domain 90193 - Notch domain	0	Direct
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00002369	Direct
55874,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 domain 2-like	0.00008759	Direct
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like	0.00161	Inherited
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.001711	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.001711	Inherited
52540,90123 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region	0.00266	Inherited
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0.007047	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.03533	Inherited
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.05347	Inherited
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.07636	Inherited
57184,57196 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.09153	Inherited
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.1405	Inherited
48552,48552 48552 - Serum albumin-like 48552 - Serum albumin-like	0.1405	Inherited
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.1472	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1718	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
47986,47986,52129 47986 - DEATH domain 47986 - DEATH domain 52129 - Caspase-like	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.001711	Inherited
90123,52540,90123 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region	0.00266	Inherited
52540,90123,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00266	Inherited
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.02125	Inherited
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.02262	Inherited
49899,57196,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin 57196 - EGF/Laminin	0.02557	Inherited
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.07636	Inherited
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.08636	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1472	Inherited
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.1765	Inherited