Table 2 Integrative annotation for case studies.
Gene | Position | Annotation | Variable | Value | Service |
|---|---|---|---|---|---|
EGFR | Gene level | Cellular Component | Endosome membrane | neXtProt/MGI | |
Plasma membrane | neXtProt/MGI | ||||
basolateral plasma membrane | neXtProt/MGI | ||||
Reaction | EGFR dimerization | ProKinO | |||
Complex | EGF:EGFR dimer [plasma membrane] | ProKinO | |||
L1-EGFR trans-heterodimer | PRO | ||||
Pathway | Constitutive PI3K/AKT Signaling in Cancer | ProKinO | |||
Molecular Function | protein localization to nucleus | PRO | |||
Protein binding | neXtProt/MGI | ||||
Protein phosphatase binding | neXtProt/MGI | ||||
Biological Process | Positive regulation of cell proliferation | neXtProt/MGI | |||
epidermal growth factor receptor signaling pathway | neXtProt/MGI | ||||
Phenotype | dilated respiratory conducting tubes | MGI | |||
respiratory distress | MGI | ||||
abnormal lung interstitium morphology | MGI | ||||
abnormal lung development | MGI | ||||
S768 | Residue level(General) | PKA Position | 98 | ProKinO | |
Motif | N-lobe | ProKinO | |||
C_helix | ProKinO | ||||
subdomainIII | ProKinO | ||||
Residue level(Mutation) | Mutation Count | 252 | ProKinO | ||
Mutant Type (MT) | I | ProKinO/neXtProt | |||
G | ProKinO/neXtProt | ||||
SNP | (MT = ’I’) rs397517108 | neXtProt | |||
(MT = ’I’) rs121913465 | neXtProt | ||||
(MT = ’G’) rs756614898 | neXtProt | ||||
Mutation Description | (MT = ’I’) higher levels of basal autophosphorylation | neXtProt | |||
Residue level(PTM) | Proteoform | PR:000049851; S768-phosphorylated form; inhibitory effect on EGFR kinase activity | PRO | ||
Modification | Phosphorylation | PRO/iPTMnet | |||
Enzyme | CAMK2A | iPTMnet | |||
Equivalent Mouse Site | Q01279 S770: no evidence for modification | iPTMnet | |||
PRKCB(PKCβ) | Gene level | Cellular Component | Cytoplasm | neXtProt/MGI | |
Plasma membrane | neXtProt/MGI | ||||
Reaction | PRKCB binds diacylglycerol and phosphatidylserine | ProKinO | |||
Complex | Activated PKC beta [plasma membrane] | ProKinO | |||
Pathway | Glioma | neXtProt | |||
Pathways in cancer | neXtProt | ||||
VEGFR2 mediated cell proliferation | neXtProt | ||||
Biological Process | Positive regulation of B cell receptor signaling pathway | neXtProt/MGI | |||
Positive regulation of I-kappaB kinase/NF-kappaB signaling | neXtProt/MGI | ||||
Positive regulation of NF-kappaB transcription factor activity | neXtProt/MGI | ||||
Positive regulation of vascular endothelial growth factor receptor signaling pathway | neXtProt/MGI | ||||
Positive regulation of angiogenesis | neXtProt/MGI | ||||
S661 (S660 in PKCβII) | Residue level(General) | Functional Domain | AGC-kinase C-terminal | neXtProt | |
Residue level(Mutation) | Mutation Count | 6 | ProKinO | ||
Mutant Type (MT) | F | ProKinO | |||
C | ProKinO/neXtProt | ||||
Residue level(PTM) | Proteoform | PR:000049877; S654 & S660- phosphorylated isoform-betaII; mouse | PRO | ||
PR:000049878; S660 & S664- phosphorylated isoform-betaII | PRO | ||||
PR:000049879; S660 & S673- phosphorylated isoform-betaII; mouse | PRO | ||||
Modification | Phosphorylation | PRO/iPTMnet | |||
Enzyme | PRKCB | iPTMnet | |||
Equivalent Mouse Site | P68404 Prkcb S660; phosphorylated | PRO/iPTMnet | |||
T642 & S661(T641 & S660 in PKCβII) | Residue level(PTM) | Proteoform | PR:000049855; T500, T641, S660-phosphorylated PRKCB-2; increased protein phosphorylation; increased localization to cytoplasm | PRO | |
Modification | Phosphorylation | PRO | |||
PRKCQ(PKCθ) | Gene level | Cellular Component | Cytoplasm | MGI | |
Plasma membrane | MGI | ||||
Reaction | Autophosphorylation of PKC-theta | ProKinO | |||
Complex | Active PKC theta bound to DAG [plasma membrane] | ProKinO | |||
Biological Process | Negative regulation of T cell apoptotic process | neXtProt/MGI | |||
Positive regulation of T cell activation | neXtProt/MGI | ||||
Positive regulation of T cell proliferation | neXtProt/MGI | ||||
Positive regulation of telomerase activity | neXtProt | ||||
Positive regulation of telomere maintenance via telomerase | neXtProt | ||||
S695 | Residue level(General) | Functional Domain | AGC-kinase C-terminal | neXtProt | |
Residue level(Mutation) | Mutation Count | 1 | ProKinO | ||
Mutant Type (MT) | F | ProKinO/neXtProt | |||
Residue level(PTM) | Proteoform | PR:000049857; S695-phosphorylated form; increased protein serine/threonine kinase activity | PRO | ||
Modification | Phosphorylation | PRO/iPTMnet | |||
Equivalent Mouse Site | Q02111 S695; phosphorylated | iPTMnet |
