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Biological Pathway Taxonomy
Last uploaded:
March 30, 2022
Acronym | BPT |
Visibility | Public |
Description | Biological Pathway Taxonomy (BPT) - hierarchical taxonomy of cellular and molecular mechanisms, metabolic reactions, and diseases that can be shown as signaling pathways. BPT was created manually based on the Elsevier Pathway Collection available for public usage. There are 3 types of entities in BPT – pathway, group, and folder of pathways and groups. Group is the list of genes and proteins associated with biological function and diseases. Pathway is an interactive model of molecular interactions in human and mammalian cells described in the literature. Each model was reconstructed based on facts published in peer-reviewed journals, with manually quality control. BPT pathway entity includes several properties such as link to the model in Pathway Studio software which allows reading supported sentences from published articles and additional information about members. A list of members for each model can be provided by request. Property “network” describes maps without logical causal relationships between members to distinguish them from actual models of molecular mechanisms (“signaling”). The index folder contains all pathways and groups sorted alphabetically. |
Status | Alpha |
Format | OBO |
Contact | Anastasia Nesterova, nesterova.anastasia@gmail.com |
Categories | Biological Process, Cell, Health, Immunology, Protein, Subcellular |
Version | Released | Uploaded | Downloads |
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synonymes2022 (Parsed, Indexed, Metrics, Annotator, Error Diff) | 03/29/2022 | 03/30/2022 | OBO | CSV | RDF/XML |
2022 (Archived) | 03/29/2022 | 03/29/2022 | OBO |
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Id | urn:agi-pathway:uuid-620d64b9-e93b-42a4-ab5b-50f3f36edd38
urn:agi-pathway:uuid-620d64b9-e93b-42a4-ab5b-50f3f36edd38
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Preferred Name | B-Cell Acute Lymphoblastic Leukemia |
Synonyms |
PathwayType: signaling
PMID: 23023711
PMID: 15098032
Tissue: blood
CellType: cancer cell
CellType: B-cell
Organ_System: hematological system
Notes: Headnote: B-cell lymphoblastic leukemia (B-ALL) is a malignant neoplasm derived from B-cell progenitors. B-ALL is most commonly a childhood malignancy, but it can occur at any age.B-ALL is classified into subgroups based on the stage of neoplasm B-cell differentiation: pre-pre-B ALL (pro-B ALL), common ALL (cALL), and pre-B ALL.The clinical presentation is variable: fever, fatigue, bone pain, arthralgia, headache, vomiting, and alteration of mental status can be observed. Rarely, patients are asymptomatic. B-ALL is diagnosed initially by routine peripheral blood smear examination. Lymphadenopathy, hepatosplenomegaly, and other extramedullary sites of disease are common, with a predilection for the central nervous system and testes involvement. B-ALL cases usually carry a primary genetic event, often a chromosome translocation, and a constellation of secondary genetic alterations. Recurrent cytogenetic abnormalities occur in 80% of children and in 60-70% of adults with B-ALL. The various forms of B-ALL can be differentiated by their gene expression profiles, which are highly associated with specific chromosomal alterations. Signaling description: MLL gene rearrangements occur in approximately two thirds of infantile ALL cases. MLL is a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The MLL fusion gene, MLL-AF4, contains more than 50% of the rearrangements in pediatric B-ALL cases and occurs in only 4-8% of adult B-ALL cases. It activates HOXA7 and thereby drives leukemic progression. Another fusion gene that occurs in B-ALL is TEL-AML, which is frequent in pediatric cases (30%), but is rare in adults. TEL-AML1 induces a B-cell differentiation arrest and promotes self-renewal in B- cell progenitors. Furthermore, the BCR-ABL1 gene rearrangement is relatively rare (3%) in pediatric patients, but is a common (25%) cytogenetic abnormality in adults. BCR-ABL1 activates SRC, LYN, HCK, and FGR kinases leading to the downstream activation of PI3K/Akt. BCR-ABL1 also activates the RAS/MAPK pathway. In addition, the E2A-HLF oncogenic fusion protein promotes progenitor B-cell survival by up-regulating LMO2 expression and activating the apoptotic inhibitor, BCL2. Another fusion gene, E2A-PBX1, enhances the expression of BMI-1, a lymphoid oncogene whose product functions as a transcriptional repressor of CDKN2A. Deletion of CDKN2A/B is present in 21-36% of pediatric B-ALL and nearly 50% of adult and adolescent B-ALL cases resulting in increased cell proliferation. Deletions and mutations of PAX5, RAG1/2, IKZF1/3, TCF3, BLNK, CREBBP, and LEF1 impair B-cell differentiation, while mutations of RB1 lead to cell cycle progression. In addition, mutations of TP53 lead to apoptosis impairment. In P2RY8-CRLF2 translocation, CRLF1 and JAK2 activating mutations are strongly associated with B-ALL of Down syndrome patients, but these genetic changes are also observed in non-Down syndrome patients at a much lower rate. Outcome effects: The resulting events are block of differentiation and apoptosis, as well as uncontrolled proliferation which all lead to B-ALL progression. Highlighted proteins: Proteins with increased expression or activity are highlighted in red, and proteins with decreased expression or activity are highlighted in blue.
Description: B-cell lymphoblastic leukemia (B-ALL) is a malignant neoplasm derived from B-cell progenitors. B-ALL is most commonly a childhood malignancy but it can occur at any age. Pathway is built manually using published studies.
Tissue: bone marrow
PMID: 22575265
Link: https://mammal-profservices.pathwaystudio.com/app/sd?urn=urn:agi-pathway:uuid-620d64b9-e93b-42a4-ab5b-50f3f36edd38
NodeType: Pathway
CellType: lymphoblast
Pathway_Author: S. Sozin www.researchgate.net/profile/Sergey-Sozin
PMID: 22730540
PMID: 20807819
Source: Diseases
PMID: 21149616
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Type | http://www.w3.org/2002/07/owl#Class |
All Properties
label | B-Cell Acute Lymphoblastic Leukemia
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prefLabel | B-Cell Acute Lymphoblastic Leukemia
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database_cross_reference |
PS:PathwayType
PS:Description
PS:Tissue
PS:Pathway_Author
PS:Link
PS:CellType
PS:Organ_System
PS:PMID
PS:NodeType
PS:Notes
PS:Source
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notation | uuid-620d64b9-e93b-42a4-ab5b-50f3f36edd38
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id | urn:agi-pathway:uuid-620d64b9-e93b-42a4-ab5b-50f3f36edd38
|
subClassOf |
urn:agi-folder:b
urn:agi-folder:hematological_system
urn:agi-folder:blood
urn:agi-folder:b-cell_acute_lymphoblastic_leukemia
|
type | |
has_exact_synonym | PathwayType: signaling
PMID: 23023711
PMID: 15098032
Tissue: blood
CellType: cancer cell
CellType: B-cell
Organ_System: hematological system
Notes: Headnote: B-cell lymphoblastic leukemia (B-ALL) is a malignant neoplasm derived from B-cell progenitors. B-ALL is most commonly a childhood malignancy, but it can occur at any age.B-ALL is classified into subgroups based on the stage of neoplasm B-cell differentiation: pre-pre-B ALL (pro-B ALL), common ALL (cALL), and pre-B ALL.The clinical presentation is variable: fever, fatigue, bone pain, arthralgia, headache, vomiting, and alteration of mental status can be observed. Rarely, patients are asymptomatic. B-ALL is diagnosed initially by routine peripheral blood smear examination. Lymphadenopathy, hepatosplenomegaly, and other extramedullary sites of disease are common, with a predilection for the central nervous system and testes involvement. B-ALL cases usually carry a primary genetic event, often a chromosome translocation, and a constellation of secondary genetic alterations. Recurrent cytogenetic abnormalities occur in 80% of children and in 60-70% of adults with B-ALL. The various forms of B-ALL can be differentiated by their gene expression profiles, which are highly associated with specific chromosomal alterations. Signaling description: MLL gene rearrangements occur in approximately two thirds of infantile ALL cases. MLL is a transcriptional coactivator that plays an essential role in regulating gene expression during early development and hematopoiesis. The MLL fusion gene, MLL-AF4, contains more than 50% of the rearrangements in pediatric B-ALL cases and occurs in only 4-8% of adult B-ALL cases. It activates HOXA7 and thereby drives leukemic progression. Another fusion gene that occurs in B-ALL is TEL-AML, which is frequent in pediatric cases (30%), but is rare in adults. TEL-AML1 induces a B-cell differentiation arrest and promotes self-renewal in B- cell progenitors. Furthermore, the BCR-ABL1 gene rearrangement is relatively rare (3%) in pediatric patients, but is a common (25%) cytogenetic abnormality in adults. BCR-ABL1 activates SRC, LYN, HCK, and FGR kinases leading to the downstream activation of PI3K/Akt. BCR-ABL1 also activates the RAS/MAPK pathway. In addition, the E2A-HLF oncogenic fusion protein promotes progenitor B-cell survival by up-regulating LMO2 expression and activating the apoptotic inhibitor, BCL2. Another fusion gene, E2A-PBX1, enhances the expression of BMI-1, a lymphoid oncogene whose product functions as a transcriptional repressor of CDKN2A. Deletion of CDKN2A/B is present in 21-36% of pediatric B-ALL and nearly 50% of adult and adolescent B-ALL cases resulting in increased cell proliferation. Deletions and mutations of PAX5, RAG1/2, IKZF1/3, TCF3, BLNK, CREBBP, and LEF1 impair B-cell differentiation, while mutations of RB1 lead to cell cycle progression. In addition, mutations of TP53 lead to apoptosis impairment. In P2RY8-CRLF2 translocation, CRLF1 and JAK2 activating mutations are strongly associated with B-ALL of Down syndrome patients, but these genetic changes are also observed in non-Down syndrome patients at a much lower rate. Outcome effects: The resulting events are block of differentiation and apoptosis, as well as uncontrolled proliferation which all lead to B-ALL progression. Highlighted proteins: Proteins with increased expression or activity are highlighted in red, and proteins with decreased expression or activity are highlighted in blue.
Description: B-cell lymphoblastic leukemia (B-ALL) is a malignant neoplasm derived from B-cell progenitors. B-ALL is most commonly a childhood malignancy but it can occur at any age. Pathway is built manually using published studies.
Tissue: bone marrow
PMID: 22575265
Link: https://mammal-profservices.pathwaystudio.com/app/sd?urn=urn:agi-pathway:uuid-620d64b9-e93b-42a4-ab5b-50f3f36edd38
NodeType: Pathway
CellType: lymphoblast
Pathway_Author: S. Sozin www.researchgate.net/profile/Sergey-Sozin
PMID: 22730540
PMID: 20807819
Source: Diseases
PMID: 21149616
See more
See less
|
treeView |
urn:agi-folder:b
urn:agi-folder:hematological_system
urn:agi-folder:blood
urn:agi-folder:b-cell_acute_lymphoblastic_leukemia
|
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