Spreadsheet: 54d2bdaf-9950-481e-9552-aeeef9367c5c
Sheet: Sheet1

BIN | MGI_ID | [NAME] | GO_ID | GO term | would be annotated | likely to be true | unclear | seems unlikely | very unlikely or not true | already annotated | reasons
 | MGI:95688 | Gdf5 | GO:0001501 | skeletal development | X |  |  |  |  |  | IMP|MGI:1855972|J:19596
 | MGI:95688 | Gdf5 | GO:0007368 | determination of left/right symmetry |  |  |  | X |  |  | dorsal ventral and proximal distal have been shown by IMP
 | MGI:95688 | Gdf5 | GO:0007369 | gastrulation |  |  |  |  | X |  | I find no evidence for this.
 | MGI:95688 | Gdf5 | GO:0007498 | mesoderm development |  |  |  |  | X
 | MGI:95688 | Gdf5 | GO:0009799 | determination of symmetry |  |  |  | X |  |  | As in above, evidence points to this gene product in patterning along an axis, but not in symmetry or asymmetry.
 | MGI:95688 | Gdf5 | GO:0009855 | determination of bilateral symmetry |  |  |  | X
 | MGI:95688 | Gdf5 | GO:0009968 | negative regulation of signal transduction
 | MGI:95688 | Gdf5 | GO:0017015 | regulation of transforming growth factor beta receptor signaling pathway |  |  |  |  | X |  | In GO BMPR pathways and TGFBR pathways are sibs. Although they are realted families of proteins, the pathways they describe are separate.
 | MGI:95688 | Gdf5 | GO:0030510 | regulation of BMP signaling pathway |  |  |  | X |  |  | Evidence (IGI, J:59282) shows it is a ligand for a BMPR, so although not entirely accurate, this call is not unreasonable.
 | MGI:95688 | Gdf5 | GO:0030514 | negative regulation of BMP signaling pathway |  |  |  | X |  |  | Evidence (IGI, J:59282) shows it is a ligand for a BMPR so if any interpretation of regulation is made, it would be postitive regulation.
 | MGI:95688 | Gdf5 | GO:0040007 | growth | X |  |  |  |  |  | The annotation would probably be made to a more information-rich term, but the product of this gene is involved in cartilage growth in the joints.
 | MGI:96669 | Kcn3 | GO:0001505 | regulation of neurotransmitter levels | X |  |  |  |  |  | [NAME]
 | MGI:96669 | Kcn3 | GO:0007269 | neurotransmitter secretion | X |  |  |  |  |  | [NAME]
 | MGI:96669 | Kcn3 | GO:0045055 | regulated secretory pathway | X |  |  |  |  |  | [NAME]
 | MGI:2149820 | Nans | GO:0001755 | neural crest cell migration |  | X |  |  |  |  | N-acetylneuraminic acid (sialic acid) is an important component of cell surface receptors and is found on subsets of NC cells.
 | MGI:2149820 | Nans | [NAME] | neuron maturation |  | X |  |  |  |  | N-acetylneuraminic acid (sialic acid) is an important component of cell surface receptors. I could envision that it is involved in neuron maturation.
 | MGI:2443878 | Slc4a7 | GO:0006885 | regulation of pH | X |  |  |  |  |  | IMP|J:118990
 | MGI:2443878 | Slc4a7 | GO:0015698 | inorganic anion transport | X |  |  |  |  |  | IMP|J:118990
 | MGI:2139434 | Mylk2 | GO:0006936 | muscle contraction | X |  |  |  |  |  | IMP|J:104384
 | MGI:2139434 | Mylk2 | GO:0006941 | striated muscle contraction | X |  |  |  |  |  | IMP|J:104384
 | MGI:2139434 | Mylk2 | GO:0030832 | regulation of actin filament length |  |  |  | X
 | [NAME] | Map3k4 | GO:0065009 | regulation of a molecular function |  |  |  |  | x |  | this term is a grouping term needed for is_a completeness, and should never be used for annotation.
 | MGI:2448355 | Hist2h3c1 | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | A histone is IN a protein DNA complex, but I would not call it involved in the process of assembly
 | MGI:2448436 | Hist1h4j | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:2448432 | Hist1h4i | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:2448375 | Hist1h2ba | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:1349430 | Eif2s3y | GO:0065004 | protein-DNA complex assembly |  |  | x |  | no |  | IEA to translation factor; no lit.
 | MGI:2448285 | Hist1h2aa | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | A histone is IN a protein DNA complex, but I would not call it involved in the process of assembly
 | MGI:2448306 | Hist1h2ab | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:1922442 | [NAME] | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:2448355 | Hist2h3c1 | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:2448436 | Hist1h4j | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:2448432 | Hist1h4i | GO:0065004 | protein-DNA complex assembly |  |  |  |  | x |  | as above
 | MGI:2181667 | Bbc3 | GO:0065002 | intracellular protein transport across a membrane |  |  |  | x
 | MGI:2441671 | Gpr81 | GO:0065002 | intracellular protein transport across a membrane |  |  | x |  |  |  | Ifligand is a protein, maybe
 | MGI:2147319 | Svil | GO:0065002 | intracellular protein transport across a membrane |  |  | x |  |  |  | IEApredict involvment in actin / membrane cytoskeleton
 | MGI:97847 | Raf1 | GO:0065002 | intracellular protein transport across a membrane |  |  |  | x |  |  | no membrane annotations; kinase
 | [NAME] | Iqgap1 | GO:0055002 | striated muscle cell development |  |  |  | x
 | MGI:1923847 | Gins4, | GO:0055002 | striated muscle cell development |  |  | x |  |  |  | binds protein and is in nucleus and cyto
 | MGI:1923847 | Gins4, | GO:0055001 | muscle cell development |  |  | x |  |  |  | binds protein and is in nucleus and cyto
 | MGI:2441671 | Gpr81, | GO:0051924 | regulation of calcium ion transport |  |  | x |  |  |  | maybe
 | MGI:1349479 | Chst4 | GO:0002274 | [NAME] activation |  |  |  |  | X |  | This is an enzyme which modifies carbohydrate chains attached to proteins.  A secondary effect of this is control of [NAME] dependent upon recognition of particular glycosylation motifs generated by the action of this enzyme and seen on cell surface glycoproteins.  Cellular activation does result from lymphocyte recognition of these motifs, but not from any direct binding, enzymatic action, or signal transduction performed by Chst4.
 | MGI:1349479 | Chst4 | GO:0002478 | antigen processing and presentation of exogenous peptide antigen |  |  |  | X |  |  | No literature evidence even hinting at a role here.  The type of glycosylation modification done by Chst4 has not been shown or investigated for any role in antigen presentation.
 | MGI:1349479 | Chst4 | GO:0002495 | antigen processing and presentation of peptide antigen via MHC class II |  |  |  | X |  |  | No literature evidence even hinting at a role here.  The type of glycosylation modification done by Chst4 has not been shown or investigated for any role in antigen presentation.
 | MGI:1349479 | Chst4 | GO:0002504 | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II |  |  |  | X |  |  | No literature evidence even hinting at a role here.  The type of glycosylation modification done by Chst4 has not been shown or investigated for any role in antigen presentation.
 | MGI:1349479 | Chst4 | GO:0006909 | phagocytosis |  |  |  |  | X |  | No literature evidence for this.  This enzyme could potential modify glycosylation motifs that would later be recognized by a receptor on a phagocytic cell, but this would be an upstream effect, not a direct effect.
 | MGI:1349479 | Chst4 | GO:0006911 | phagocytosis, engulfment |  |  |  |  | X |  | No literature evidence for this.  This enzyme could potential modify glycosylation motifs that would later be recognized by a receptor on a phagocytic cell, but this would be an upstream effect, not a direct effect.
 | MGI:1349479 | Chst4 | GO:0007009 | plasma membrane organization and biogenesis |  |  |  |  | X |  | This is an enzyme which modifies carbohydrate chains attached to proteins.  It has no known role in lipid synthesis or trafficking, and given its known enzymatic activity, it is unlikely to have such a role.
 | MGI:1349479 | Chst4 | GO:0019884 | antigen processing and presentation of exogenous antigen |  |  |  | X |  |  | No literature evidence even hinting at a role here.  The type of glycosylation modification done by Chst4 has not been shown or investigated for any role in antigen presentation.
 | MGI:1349479 | Chst4 | GO:0019886 | antigen processing and presentation of exogenous peptide antigen via MHC class II |  |  |  | X |  |  | No literature evidence even hinting at a role here.  The type of glycosylation modification done by Chst4 has not been shown or investigated for any role in antigen presentation.
 | MGI:1349479 | Chst4 | GO:0030100 | regulation of endocytosis |  |  |  |  | X |  | No literature evidence for this.  This enzyme could potential modify glycosylation motifs that would later be recognized by a receptor triggering endocytosis, but this would not be a direct regulation event.
 | MGI:1349479 | Chst4 | GO:0045807 | positive regulation of endocytosis |  |  |  |  | X |  | No literature evidence for this.  This enzyme could potential modify glycosylation motifs that would later be recognized by a receptor triggering endocytosis, but this would not be a direct regulation event.
 | MGI:1349479 | Chst4 | GO:0048002 | antigen processing and presentation of peptide antigen |  |  |  | X |  |  | No literature evidence even hinting at a role here.  The type of glycosylation modification done by Chst4 has not been shown or investigated for any role in antigen presentation.
 | MGI:1349479 | Chst4 | GO:0050764 | regulation of phagocytosis |  |  |  |  | X |  | No literature evidence for this.  This enzyme could potential modify glycosylation motifs that would later be recognized by a receptor on a phagocytic cell, but this would be an upstream effect, not a direct regulation event.
 | MGI:1349479 | Chst4 | GO:0050766 | positive regulation of phagocytosis |  |  |  |  | X |  | No literature evidence for this.  This enzyme could potential modify glycosylation motifs that would later be recognized by a receptor on a phagocytic cell, but this would be an upstream effect, not a direct regulation event.
 | MGI:1349479 | Chst4 | GO:0051050 | positive regulation of transport |  |  |  | X |  |  | This is an enzyme which modifies carbohydrate chains attached to proteins.  It has no known role direct role in transport, but this is such a broad category I can't role it out completely.
 | MGI:109355 | Stx1a | GO:0006887 | exocytosis | X |  |  |  |  |  | This is a long-demostrated role for Stx1a (PMID:7690687) -- unsure if mouse gp-specific data exists.
 | MGI:109355 | Stx1a | GO:0006944 | membrane fusion | X |  |  |  |  |  | Members of this protein family are involved in promoting membrane fusion events. Not sure if direct evidence for mouse Stx1a exists, but at least an ISS is possible.
 | MGI:109355 | Stx1a | GO:0016079 | synaptic vesicle exocytosis | X |  |  |  |  |  | This is a long-demostrated role for Stx1a (PMID:7690687) -- unsure if mouse gp-specific data exists.
 | MGI:109355 | Stx1a | GO:0017156 | calcium ion-dependent exocytosis | X |  |  |  |  |  | Stated in abstract of PMID: 16123365 -- unsure if mouse gp-specific data exists.
 | MGI:109355 | Stx1a | GO:0048489 | synaptic vesicle transport | X |  |  |  |  |  | This is a long-demostrated role for Stx1a (PMID:7690687) -- unsure if mouse gp-specific data exists.
 | MGI:109355 | Stx1a | GO:0051650 | establishment of vesicle localization | X |  |  |  |  |  | Related term to GO:0048489 -- would coannotate.
 | [NAME] | Mzf1 | GO:0002200 | somatic diversification of immune receptors |  |  |  |  | X |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which shows normal lymphocyte development in the KO, which would not be expected a gene involved in this process.  Similarly, published expression data say this gene is expressed primarily in myeloid, not lymphocyte lineages.
 | [NAME] | Mzf1 | GO:0002377 | immunoglobulin production |  |  |  |  | X |  | No evidence in literature; see above comment.
 | [NAME] | Mzf1 | GO:0002440 | production of molecular mediator of immune response |  |  |  | X |  |  | No evidence in literature; gene has been shown to control cell proliferation of myeloid cells.
 | [NAME] | Mzf1 | GO:0002562 | somatic diversification of immune receptors via germline recombination within a single locus |  |  |  |  | X |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which shows normal lymphocyte development in the KO, which would not be expected a gene involved in this process.  Similarly, published expression data say this gene is expressed primarily in myeloid, not lymphoid lineages.
 | [NAME] | Mzf1 | GO:0002761 | regulation of myeloid [NAME] differentiation |  |  | X |  |  |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which states directly that this gene controls proliferation of myeloid cells, but not differentiation of myeloid lineages.  However a couple earlier papers doing in vitro studies in human and mouse systems suggest it may have a role in differentiation of specific myeloid lineages.
 | [NAME] | Mzf1 | GO:0007050 | cell cycle arrest |  |  | X |  |  |  | Depends how broadly one interprets the data of PMID:11445537 and the definition of GO:0007050.
 | [NAME] | Mzf1 | GO:0007093 | mitotic checkpoint |  |  |  | X |  |  | Seems unlikely as Mzf1 is thought to be a transcription factor.
 | [NAME] | Mzf1 | GO:0016444 | somatic cell DNA recombination |  |  |  |  | X |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which shows normal lymphocyte development in the KO, which would not be expected a gene involved in this process.  Similarly, published expression data say this gene is expressed primarily in myeloid, not lymphoid lineages.
 | [NAME] | Mzf1 | GO:0016445 | somatic diversification of immunoglobulins |  |  |  |  | X |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which shows normal lymphocyte development in the KO, which would not be expected a gene involved in this process.  Similarly, published expression data say this gene is expressed primarily in myeloid, not lymphoid lineages.
 | [NAME] | Mzf1 | [NAME] | somatic recombination of immunoglobulin gene segments |  |  |  |  | X |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which shows normal lymphocyte development in the KO, which would not be expected a gene involved in this process.  Similarly, published expression data say this gene is expressed primarily in myeloid, not lymphoid lineages.
 | [NAME] | Mzf1 | GO:0045577 | regulation of B cell differentiation |  |  |  |  | X |  | This is contra-indicated by PMID:11445537, the KO mouse paper for the gene, which shows normal lymphocyte development in the KO, which would not be expected a gene involved in this process.  Similarly, published expression data say this gene is expressed primarily in myeloid, not lymphoid lineages.
 | [NAME] | Mzf1 | GO:0045786 | negative regulation of progression through cell cycle |  |  | X |  |  |  | Depends how broadly one interprets the data of PMID:11445537 and the definition of GO:0007050.
 | [NAME] | Mzf1 | GO:0051047 | positive regulation of secretion |  |  |  | X |  |  | Seems unlikely as Mzf1 is thought to be a transcription factor.
 | MGI:95499 | Fcgr2b | GO:0002699 | positive regulation of immune effector process |  |  |  |  | X |  | If anything, we would expect negative regulation terms for this gene, due to the "ITIM" motif in its cytoplasmic tail and its known negative regulation of cell activation.
 | MGI:95499 | Fcgr2b | GO:0002705 | positive regulation of leukocyte mediated immunity |  |  |  |  | X |  | If anything, we would expect negative regulation terms for this gene, due to the "ITIM" motif in its cytoplasmic tail and its known negative regulation of cell activation.
 | MGI:95499 | Fcgr2b | GO:0002708 | positive regulation of lymphocyte mediated immunity |  |  |  |  | X |  | If anything, we would expect negative regulation terms for this gene, due to the "ITIM" motif in its cytoplasmic tail and its known negative regulation of cell activation.
 | MGI:95499 | Fcgr2b | GO:0002761 | regulation of myeloid [NAME] differentiation |  | X |  |  |  |  | Supported by PMID:15843524, but would annotate to a more specific term in practice.
 | MGI:95499 | Fcgr2b | GO:0002821 | positive regulation of adaptive immune response |  |  |  |  | X |  | If anything, we would expect negative regulation terms for this gene, due to the "ITIM" motif in its cytoplasmic tail and its known negative regulation of cell activation.
 | MGI:95499 | Fcgr2b | GO:0002824 | positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains |  |  |  |  | X |  | If anything, we would expect negative regulation terms for this gene, due to the "ITIM" motif in its cytoplasmic tail and its known negative regulation of cell activation.
 | MGI:95499 | Fcgr2b | GO:0045639 | positive regulation of myeloid cell differentiation |  |  |  | X |  |  | Contraindicated by PMID:15843524, but conceivably possible.
 | MGI:95499 | Fcgr2b | GO:0045670 | regulation of osteoclast differentiation |  |  |  | X |  |  | No evidence in literature.
 | MGI:95499 | Fcgr2b | GO:0046850 | regulation of bone remodeling |  |  |  | X |  |  | No evidence in literature.
 | MGI:95499 | Fcgr2b | GO:0046851 | negative regulation of bone remodeling |  |  |  | X |  |  | No evidence in literature.
 | MGI:1888506 | Retn | GO:0006006 | [NAME] process | X |  |  |  |  |  | Supported by PMID:17065346, although a regulation term would be better.
 | MGI:1888506 | Retn | GO:0006090 | pyruvate metabolic process |  |  |  | X |  |  | No evidence in literature.
 | MGI:1888506 | Retn | GO:0006638 | neutral lipid metabolic process |  |  | X |  |  |  | PMID:15358276 and other suggest indirect effects on lipid metabolism -- not sure if this is the correct term to annotate to.
 | MGI:1888506 | Retn | GO:0006639 | [NAME] process |  |  | X |  |  |  | PMID:15358276 and other suggest indirect effects on lipid metabolism -- not sure if this is the correct term to annotate to.
 | MGI:1888506 | Retn | GO:0006641 | triacylglycerol metabolic process |  |  | X |  |  |  | PMID:15358276 and other suggest indirect effects on lipid metabolism -- not sure if this is the correct term to annotate to.
 | MGI:1888506 | Retn | GO:0006662 | glycerol ether metabolic process |  |  |  | X |  |  | No evidence in literature.
 | MGI:1888506 | Retn | GO:0016051 | carbohydrate biosynthetic process |  | X |  |  |  |  | A more specific regulation term would be a better choice (PMID: 15684405).
 | MGI:1888506 | Retn | GO:0019319 | hexose biosynthetic process |  | X |  |  |  |  | A regulation term would be a better choice (PMID: 15684405).
 | MGI:1888506 | Retn | GO:0042593 | glucose homeostasis | X |  |  |  |  |  | Supported by PMID:17065346.
 | MGI:1888506 | Retn | GO:0046165 | alcohol biosynthetic process |  | X |  |  |  |  | A more specific regulation term would be a better choice (PMID: 15684405).
 | MGI:1888506 | Retn | GO:0046364 | monosaccharide biosynthetic process |  | X |  |  |  |  | A more specific regulation term would be a better choice (PMID: 15684405).
 | MGI:1888506 | Retn | GO:0046486 | glycerolipid metabolic process |  |  |  | X |  |  | No evidence in literature.
 | MGI:1888506 | Retn | GO:0051241 | negative regulation of multicellular organismal process |  |  |  | X |  |  | Term is too non-specific.
 | MGI:1343461 | Ecel1 | GO:0006956 | complement activation |  |  |  | X |  |  | No evidence in literature. [NAME] is at least a peptidase.
 | MGI:1343461 | Ecel1 | GO:0007613 | memory |  |  |  |  | X |  | No evidence in literature.
 | MGI:1343461 | Ecel1 | GO:0048168 | regulation of neuronal synaptic plasticity |  |  |  |  | X |  | No evidence in literature.
 | MGI:1343461 | Ecel1 | GO:0002541 | activation of plasma proteins during acute inflammatory response |  |  |  | X |  |  | No evidence in literature. [NAME] is at least a peptidase.