Here we build a list of experimental motif definitions to serve as the basis of a classification ontology (for consultation and collaboration with OBI curators and other Big Mech participants). .
This was initiated from the list on the KEfED Modeling of Coprecipitation Ras Papers page. This is where we add definitions and maintain a definitive list + curation manual.
{
"type": "Transfect_IP_WB",
"measurements": [
{
"value": {"protein-concentration": "0/7: none"},
"context": {
"immunoprecipitate": "control",
"cell-type": " Eps8(-/-) fibroblasts",
"promoter-construct": "Eps8myc",
"primary-antibody": "Sos-1"
},
"text": "Endogenous Sos-1 and E3b1 could be detected in anti-myc
immunoprecipitates from lysates of Eps8myc-reconstituted, but not
from eps8 / fibroblasts"
},
{
"value": {"protein-concentration": "0/7: none"},
"context": {
"immunoprecipitate": "control",
"cell-type": " Eps8(-/-) fibroblasts",
"promoter-construct": "Eps8myc",
"primary-antibody": "E3b-1"
},
"text": "Endogenous Sos-1 and E3b1 could be detected in anti-myc
immunoprecipitates from lysates of Eps8myc-reconstituted, but not
from eps8 / fibroblasts"
},
{
"value": {"protein-concentration": "4/7: moderate"},
"context": {
"immunoprecipitate": "myc",
"cell-type": " Eps8(-/-) fibroblasts",
"promoter-construct": "Eps8myc",
"primary-antibody": "Sos-1"
},
"text": "Endogenous Sos-1 and E3b1 could be detected in anti-myc
immunoprecipitates from lysates of Eps8myc-reconstituted, but not
from eps8 / fibroblasts"
},
{
"value": {"protein-concentration": "4/7: moderate"},
"context": {
"immunoprecipitate": "myc",
"cell-type": " Eps8(-/-) fibroblasts",
"promoter-construct": "Eps8myc",
"primary-antibody": "E3b-1"
},
"text": "Endogenous Sos-1 and E3b1 could be detected in anti-myc
immunoprecipitates from lysates of Eps8myc-reconstituted, but not
from eps8 / fibroblasts"
}
],
"name": "11777939-Fig1B"
"methodFragment": "",
"figureFragment": "(B) Total cellular lysates (10 mg), obtained from the transfectants
described in A, were immunoprecipitated (IP) with the antibody indicated at the
bottom (ctr, irrelevant antibody), followed by immunoblot with indicated antibodies
(WB). The indicated lanes (lysates) were loaded with 100 g of total cellular
lysates.",
"resultFragment": "Endogenous Sos-1 and E3b1 could be detected in anti-myc
immunoprecipitates from lysates of Eps8myc-reconstituted, but not from eps8 /
fibroblasts",
"implicationFragment": ""
}
{
"constant-context": {
"cell-type": "293T",
},
"measurement-comparisons": [
{
"value1": {"protein-concentration": "low"},
"context1": {
"primary-antibody": "Sos-1",
"immunoprecipitate": "Grb2",
"promoter-construct": "E3b1"
},
"value2": {"protein-concentration": "high"},
"context2": {
"primary-antibody": "Sos-1",
"immunoprecipitate": "Grb2",
"promoter-construct": "control"
}
}
],
"type": "Tfx_IP_WB",
"name": "11777939-Fig3B"
"methodFragment": "This hypothesis was validated by a series of experiments performed both in vitro and in vivo.",
"figureFragment": "(B) Lysates, from 293T cells transfected (Tfx) with E3b1 or a control
vector (ctr), were immunoprecipitated (IP) with anti-Grb2 or an irrelevant
antibody (ctr), followed by detection (WB) with anti?Sos-1 (top) or anti-Grb2
(middle). The expression of E3b1 (bottom) was detected with an anti-E3b1 antibody.",
"resultFragment": "(e) overexpression of E3b1 significantly decreased the
coimmunoprecipitation between Grb2 and Sos-1 (Fig. 3 B).",
"implicationFragment": "Thus, Sos-1 binds either E3b1 or Grb2, in a mutually exclusive
fashion, suggesting that two distinct pools of Sos-1 exist in the cells.",
}