Annotation Extension Relation:results in morphogenesis of: Difference between revisions

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More examples of this usage of occurs_in can be found on the documentation page for [[Column_16:_Cell_Type]]
More examples of this usage of occurs_in can be found on the documentation page for [[Column_16:_Cell_Type]]


==== Specifying the subcellular location in which a process happens ====
1. '''Protein interaction at the sarcoplasmic reticulum:'''
Statement from paper:
''Canine cardiac junctional SR vesicles were solubilized with 2% Triton X-100 and loaded on the affinity column equilibrated in EGTA-containing buffer (Fig.1). Calsequestrin-binding proteins were then eluted in buffer containing 20 mm CaCl2, a calcium concentration sufficient to disrupt all calsequestrin protein-binding interactions. Immunoblotting of the eluted fractions with triadin antibody revealed that triadin bound completely to the column and was eluted as a discrete peak in Ca2+-containing buffer (Fig. 1 A, upper)''
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! With (col 8)
! Annotation Extension (col 16)
|-
| P12637 <span style="color:green">CASQ2</span>
| GO:0005515 <span style="color:green">protein binding</span>
| PMID:9287354
| IPI
| P82179 <span style="color:green">TRDN</span>
| occurs_in(GO:0016529 <span style="color:green">sarcoplasmic reticulum</span>)
|}
2. '''Sequestering of calcium ion at sarcoplasmic reticulum:'''
Statement from paper: 
''To characterize the effects of the new CASQ2 mutations on SR Ca2+ handling in vivo, we performed experiments in adult rat ventricular myocytes infected with adenoviral constructs. Caffeine (10 mmol/L) was applied to myocytes expressing either WT or mutant CASQ2 to evaluate the SR Ca2+-storing capacity by measurement of fluo-3 fluorescence and of Na+/Ca2+ exchange current (INCX; Figure 4A; Table 1).21 Expression of WT increased the SR Ca2+ content by 50%, whereas CASQ2 G112+5X reduced the SR content, not only as compared with WT expression but also as compared with native cells (Ad-control).'' 
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| O14958 <span style="color:green">CASQ2</span>
| GO:0051208 <span style="color:green">sequestering of calcium ion</span>
| PMID:16908766
| IMP
| occurs_in(GO:0016529 <span style="color:green">sarcoplasmic reticulum</span>), occurs_in(CL:0000746 <span style="color:green">cardiac muscle cell</span>)
|}
Note the use of the comma to create a compound annotation extension. The interpretation of this annotation is CASQ2 is involved in sequestering calcium ions in the sarcoplasmic reticulum of cardiac muscle cell.


== Using examples (from above) to demonstrate [[Folding_and_Unfolding]] using the relationship occurs_in ==
== Using examples (from above) to demonstrate [[Folding_and_Unfolding]] using the relationship occurs_in ==

Revision as of 11:42, 13 May 2014

Back to Annotation usage examples for each annotation extension relation

Definition

Identifies the cell, tissue, or anatomical entity which under goes morphogenesis.

Child terms

  • None.

Scope of use

Domain

BFO:0000007 ! process (Biological Process or Molecular Function)

Range

ENTITY_UNION:0000006 ! entity

Annotation Extension Usage Examples

Enhancing Molecular Function and Biological Process Annotations

Specifying the cell or tissue type in which a process happens

1. Differentiation of a particular cell type:

Statement from paper:

REN promoted neuronal differentiation of neural committed progenitor cells of CNS (ST14A cells, Fig. 7 A) or PNS (N2a cells, Fig. 7 B) origin.


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
MGI:2448712 Ren GO:0030154 cell differentiation PMID:12186855 IDA occurs_in(CL:0000540 neuron)


2. A protein's involvement in changing a particular cell's shape:

Statement from paper:

Eotaxin, eotaxin-2, and MCP-4 were the most potent inducers of eosinophil shape change, followed by MCP-3, while MCP-1 and IL-8 were inactive. MCP-4 alone showed a bell-shaped eosinophil dose-response curve over the dose range tested. Eotaxin and eotaxin-2 were inactive on monocytes (Fig. 2⇓B), whereas MCP-1, -3, and -4 all induced monocyte shape change, with MCP-3 exhibiting the highest potency.

Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
Q99616 MCP4 GO:0008360 regulation of cell shape PMID:10072545 IDA occurs_in(CL:0000771 eosinophil) 'pipe' occurs_in(CL:0000576 monocyte)

Note the use of the pipe to create a multiple annotation extensions. The interpretation of this annotation is MCP4 is involved in the regulation of eosinophil cell shape and monocyte cell shape.

More examples of this usage of occurs_in can be found on the documentation page for Column_16:_Cell_Type


Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship occurs_in

1. Differentiation of a particular cell type:

Folded/unfolded Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16) Parent terms of new folded GO term
Unfolded MGI:2448712 Ren GO:0030154 cell differentiation PMID:12186855 IDA occurs_in(CL:0000540 neuron)
Folded MGI:2448712 Ren New GO ID neuron cell differentiation PMID:12186855 IDA is_a cell differentiation


2. A protein's involvement in changing a particular cell's shape:

Note the use of the pipe to create a multiple annotation extensions.

Folded/unfolded Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16) Parent terms of new folded GO term
Unfolded Q99616 MCP4 GO:0008360 regulation of cell shape PMID:10072545 IDA occurs_in(CL:0000771 eosinophil) 'pipe' occurs_in(CL:0000576 monocyte)
Folded Q99616 MCP4 New GO ID regulation of eosinophil cell shape PMID:10072545 IDA is_a regulation of cell shape
Folded Q99616 MCP4 New GO ID regulation of monocyte cell shape PMID:10072545 IDA is_a regulation of cell shape

Back to Annotation usage examples for each annotation extension relation

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