Difference between revisions of "Annotation Extension Relation:causally upstream of"
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'''OWL class expression:''' | '''OWL class expression:''' | ||
regulation of gene expression AND causally_upstream_of SOME regulation of extracellular matrix assembly AND has_regulation_target SOME Fibronectin | |||
'''2. Specifying the biological process upstream of the regulation of mRNA expression levels.''' | '''2. Specifying the biological process upstream of the regulation of mRNA expression levels.''' |
Revision as of 09:16, 6 August 2014
Back to Annotation usage examples for each annotation extension relation
Definition
Process A is causally_upstream of process B if process A occurs first, and process A causes process B to happen. Processes A and B do not overlap.
Child terms
- None
Scope of use
Domain
BFO:0000007 ! process (Biological Process or Molecular Function)
Range
GO:0008150 ! GO:Biological Process
GO:0003674 ! GO:Molecular Function
Annotation Extension Usage Examples
1. Specifying the biological process upstream of the regulation of protein levels.
Summary of paper:
Transfection of RGC-32 and SMAD3 leads to an increase in the protein expression of extracellular matrix protein fibronectin. RGC-32 mediates transforming growth factor-β1-induced epithelial-mesenchymal transition (EMT) a process associated with the massive deposition of matrix and the synthesis of a fibrosis matrix.
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) |
---|---|---|---|---|---|
P84022 | SMAD3 | GO:0010468 regulation of gene expression | PMID:21307346 | IDA | causally_upstream_of GO:1901201 regulation of extracellular matrix assembly has_regulation_target(UniProtKB:P02751 FN1) Fibronectin |
P84022 | SMAD3 | GO:1901201 regulation of extracellular matrix assembly | PMID:21307346 | IDA | |
Q9H4X1 | RGCC (RGC-32) | GO:0010468 regulation of gene expression | PMID:21307346 | IDA | causally_upstream_of GO:1901201 regulation of extracellular matrix assembly has_regulation_target(UniProtKB:P02751 FN1) Fibronectin |
Q9H4X1 | RGCC (RGC-32) | GO:1901201 regulation of extracellular matrix assembly | PMID:21307346 | IDA |
2. Specifying the biological process upstream of the regulation of mRNA expression levels.
Summary of paper:
Transfection of mouse Foxa2 into rat INS-r3 cells results in blunted glucose-stimulated insulin secretion and drastically decreased mRNA levels of insulin, GLUT2 and glucokinase. In contrast, loss of Foxa2 function leads to up-regulation of hexokinase (HK) I and II and glucokinase (HK-IV) mRNA expression and down-regulation of KATP Channel Subunits Sur1 and Kir6.2 mRNA expression. High levels of the glucose transporter Glut2, enable rapid equilibration of glucose across the plasma membrane, whereas low levels of high affinity hexokinase isoforms (hexokinases I, II, and III) optimize glucose sensing in the physiological blood glucose range. Glucokinase (hexokinase IV) is rate-limiting enzyme for glucose metabolism, and determines the glucose sensing in pancreatic β-cells.
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) |
---|---|---|---|---|---|
P35583 | Foxa2 | GO:0000433 negative regulation of transcription from RNA polymerase II promoter by glucose | 11875061 | IDA | causally_upstream_of GO:2000971 negative regulation of detection of glucose has_regulation_target(UniProtKB:P52792 GCK) Glucokinase |
P35583 | Foxa2 | GO:2000971 negative regulation of detection of glucose | 11875061 | IDA |
Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship causally_upstream_of
1. Specifying the biological process upstream of the regulation of protein levels.
Summary of paper:
Transfection of RGC-32 and SMAD3 leads to an increase in the protein expression of extracellular matrix protein fibronectin. RGC-32 mediates transforming growth factor-β1-induced epithelial-mesenchymal transition (EMT) a process associated with the massive deposition of matrix and the synthesis of a fibrosis matrix.
Folded/unfolded | DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|---|
Unfolded | P84022 | SMAD3 | GO:0010468 regulation of gene expression | PMID:21307346 | IDA | causally_upstream_of GO:1901201 regulation of extracellular matrix assembly has_regulation_target(UniProtKB:P02751 FN1) Fibronectin | |
Folded | P84022 | SMAD3 | GO:0010468 regulation of gene expression | PMID:21307346 | IDA | No new GO term created |
OWL class expression:
regulation of gene expression AND causally_upstream_of SOME regulation of extracellular matrix assembly AND has_regulation_target SOME Fibronectin
2. Specifying the biological process upstream of the regulation of mRNA expression levels.
Summary of paper:
Transfection of mouse Foxa2 into rat INS-r3 cells results in blunted glucose-stimulated insulin secretion and drastically decreased mRNA levels of insulin, GLUT2 and glucokinase. In contrast, loss of Foxa2 function leads to up-regulation of hexokinase (HK) I and II and glucokinase (HK-IV) mRNA expression and down-regulation of KATP Channel Subunits Sur1 and Kir6.2 mRNA expression. High levels of the glucose transporter Glut2, enable rapid equilibration of glucose across the plasma membrane, whereas low levels of high affinity hexokinase isoforms (hexokinases I, II, and III) optimize glucose sensing in the physiological blood glucose range. Glucokinase (hexokinase IV) is rate-limiting enzyme for glucose metabolism, and determines the glucose sensing in pancreatic β-cells.
Folded/unfolded | DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) |
---|---|---|---|---|---|---|
Unfolded | P35583 | Foxa2 | GO:0000433 negative regulation of transcription from RNA polymerase II promoter by glucose | 11875061 | IDA | causally_upstream_of GO:2000971 negative regulation of detection of glucose has_regulation_target(UniProtKB:P52792 GCK) Glucokinase |
Folded | P35583 | Foxa2 | GO:0000433 negative regulation of transcription from RNA polymerase II promoter by glucose | 11875061 | IDA | No new GO term created |
OWL class expression:
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