Src (rat) review notes

Session 1 (initial review)

• Fetched with just fetch-gene rat Src; UniProt Q9WUD9 (SRC_RAT, RGD:620795, GeneID 83805)
  confirmed. 272 GOA rows. Literature synthesis in Src-deep-research-manual.md (no
  deep-research API available).
• Most cached papers are abstract-only; full text available for PMID:10884433, 19230846,
  19736311, 19948503, 20167931, 20356829, 20380727, 26026271, 28220894 and 19193640.
• Core picture: myristoylated SH3-SH2-kinase non-receptor tyrosine kinase
  [UniProtKB:Q9WUD9 "Non-receptor protein tyrosine kinase which is activated following
  engagement of many different classes of cellular receptors"]; at the plasma membrane and
  focal adhesions it relays integrin, RTK and GPCR (angiotensin II) signals; in neurons it is
  anchored to the NMDA receptor complex and up-regulates NMDA channel activity
  PMID:9005855.
• Decisions:
• Kinase MF rows (protein kinase / kinase / protein tyrosine kinase activity) MODIFY to
  GO:0004715 non-membrane spanning protein tyrosine kinase activity, the core MF.
• Bare protein binding rows REMOVE, except PMID:8849729 (SH2 binds Pyk2 pTyr402) ->
  phosphotyrosine residue binding and PMID:16352297 (SH3 binds Cav1.2 alpha1c) ->
  transmembrane transporter binding.
• Generic CC (membrane, cell junction, anchoring junction, actin-based cell projection)
  MODIFY to plasma membrane / focal adhesion / cell-cell junction / podosome.
• IEP rows on CC terms (glutamatergic synapse, postsynaptic specialization from
  PMID:14529711) get WRONG_EVIDENCE_CODE source defects (CHECK); the location itself is
  supported by the IDA rows from the same paper.
• Several IEP "response to X" / proliferation rows rest on expression or activation
  correlation only: MARK_AS_OVER_ANNOTATED.
• PMID:2462872 (PC12 growth cones) curated to dendritic growth cone / dendritic filopodium;
  PC12 neurites are not dendrites -> MODIFY to growth cone with source defect, filopodium
  row UNDECIDED.
• PMID:10698670 (testicular Src) curated to mitochondrion-derived vesicle: not supported
  by abstract -> UNDECIDED with CHECK defect.
• PMID:9227431 DNA biosynthetic process -> MODIFY to positive regulation of DNA
  biosynthetic process (Src is a signalling kinase, not a DNA synthesis enzyme).
• GO:0030331 carries an "obsolete" prefix in the GOA label, but OLS and the local GO build
  still list "nuclear estrogen receptor binding" as live; kept as non-core.
• NEW: GO:2000310 regulation of NMDA receptor activity (IDA, PMID:9005855). Src catalyses the
  regulatory phosphorylation itself, so it passes the participation test. Comparator check
  (QuickGO, GO:2000310 exact, 42 rows): the regulator kinase DAPK1 (IMP, mouse) and the
  scaffold Dlg4 (IMP, rat) carry the term, so regulatory kinases of the receptor are within
  GO convention; Fyn does not carry it, which is an absence rather than a contrary convention.
• PMID:19193640 (annexin 2 and v-Src) read in full; concerns viral Src in Rat-1 cells; used
  only as context.